NetKarma Provenance Retrieval and Visualization Plugin For
Contents
1. b Node Attribute Browser Edge Attribute Browser Network Attribute Browser Figure 6 1 3 Select the Karma provenance XML file Load the Karma provenance graph A node shape onto the network view An edge shape onto the source node then cick on the target node To add nodes and edges specified in SIF format On empty space to create rT The sample OPM graph created for file C Users peng Desktop Graph_opm xmi ts_out4 xml one Data Panel On a node to begin an edge and specify the By g feo eB bs 9 source node Then cick I ID on the target node to finish the edge O b Node Attribute Browser Edge Attribute Browser Network Attribute Browser Figure 6 1 4 Load the Karma provenance graph The initial graph will look like this your graph may differ depending on your experiment s provenance 12 Fle Eat View Select Layout Pigs Hep Tot Preece cen Karma Figure 6 1 5 Initial graph 6 2 Applying layout algorithms to the Karma provenance graph Node Atroute Browser Ege Attbute Bronse Network Atrbute Browser Right click drag to ZOOM Middle click drag to PAN Figure 6 2 1 Do hierarchy 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 G Cytoscape Desktop New Sessie File2. nodes generated by a small number of Process nodes You 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 previous figure 34 J Cytoxcape Desktop Jew 5 File Edit View Select Layout Plugins Help Tools pore ge CE EA Karma _ BL To add nodes and edges specified in SF format CTRL click On empty space to create Figure 6 12 1 2 Select processes 2 Click zoom selected region icon from the toolbar highlighted magnifying glass icon the Figure 6 8 1 3 9 ro oe Me CORSO ea Karma On empty space to create a node On a node to begin an edge and specify the source node Then cick on the target node to finish the edge Specify Identifier z Node Attrbute Bronser lick drag to ZOOM Middle click crag to PAN Figure 6 12 1 3 Zoom into process region 3 Right click on one of the nodes with a large out degree a significant number of edges 35 EY Cytozcape Desktop New Ses File Edit View Select Layout Plugins Help Tools SRRA a 5453 R oF Karma T ControlPanel tne s peng Desktop Graph_opr outi To add nodes and edges specified in SF format CTRL click On empty space to create Process_12 Visual Mapping Bypass Nested Network Use Web Services Hide Node Figure 6 12 1 4 Right cli
3. Edit View Select Layout Plugins Help Tools Q2QRQ 8 8 8 4y53R ov Karma B Control Panel f Node Attribute Browser Edge Attribute Browser Network Attribute Browser tight click drag to ZOOM Middle click drag to PAN Figure 6 2 2 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 X axis 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 File Edit View Select Plugins Help Tools SAAG im Sy Bs SB cos Karma T B Control Panel Align and Distribute MOwOret Sraph_op Settings Anode shape GENI OPMLayout An edge shap node then cig C sCape Layouts Double click To add nodes and edges specified in SIF format CTRL click On empty space to create a node On a node to begin an edge and specify the source node Then cick on the target node to finish the edge WasTriggeredBy p Data Panel BOXE 8 Eren A WasDerivedFrom used Node Attrbute Bowser Ede Attrbute Browser m Welcome to Cytoscape 2 8 0 R
4. of the imported attributes by configuring the following properties visualA ttributes configuration for the properties related to the rendering of the graph includes nodeLabel to tell which attribute of the nodes you want to show as their labels We have separated configuration for PROCESS and ARTIFACT processLabel the label of process nodes artifactLabel the label of artifact nodes Each group of configuration has a list of attribute names listed with a priority from the highest to the lowest attributeName which attribute of the nodes you want to show as their label For example if you want to use the attribute objectValue as the label of artifacts or use the attribute ID if there is no objectValue you can set up the following configuration lt artifactLabel gt lt attributeName gt object Value 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 Cytoscape Desktop New Sess A QQQQ 8 B44 43 Boo Karma a Control Panel 2 A Wer Network VizMapper ove Network No Ed gt gt Karma Server Configuration J Boss Axis2 Config ServiceURL vttp netkarma testilab qrnoc iu edu 8080 aus2 services KarmaService Rabbitmg config Data Pane O68 ID Current Session al network attributes wil be lost Do you want to continue OK
5. 1 provenance_karma If an instance of the NetKarma service either hosted as a web service or as a standalone service using the RabbitMQ messaging bus already exists contact your system administrator for obtaining access 2 2 Installation dependencies The NetKarma provenance retrieval and visualization plugin v1 0 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 plug in 1 Java Development Kit JDK v5 or v6 http java sun com 2 Cytoscape v2 8 x http www cytoscape org 3 Installing Plugin Download the plugin package as a zip file from http pti 1u edu d21 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 You can skip this step since our plugin package already includes pre build plugin jar files But if you want to build it from source code you need to set the ant properties in the file build properties To build the NetKarma visualization plugin you need to edit the file visualization OPM_visualization build properties lt Define the Cytoscape directories gt cytoscape dir C Program Files Cytoscape_v2 8 1 the directory where Cytoscape is installed on your computer In the di
6. 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 6 3 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 6 Cytoscape Desktop File Edit View Select Layout Plugins Help Tools 2G 2QN8 JEL EE Karma THB Edit Network Title Create View Destroy View Destroy Network Apply Visual Style Create WiMax Dos Vis Network comparison DCA comparison Figure 6 7 1 Right click on the network in the network control panel and then select the Create WiMax Dos Vis 21 OEE iene HD Cytoscape Desktop N sic File Edit View Select Layout Plugins Help Tools 6E QQQQ 8 9 B 4p 45 B o Karma BB pe 768 0 136 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 6 4 Navigating the Karma provenance graph 1 Double click on any node to see its attributes o Help Toots amp B QQOQ Q B S 4y 35 Bow Karma BB peng Deskto On empty space to create a node On a node to begin an s am d Li Node Attribute Browser Edge Attribute Browse
7. AQQQ 8 84255 Beek Karma CBB Control Pane ns Ty nesot naom tte rnn seron Nodes fidges sco sm generated the artifact selected in previous figure 6 10 Assign short label If you find it unsatisfying to directly select node attribute as node labels you can assign your custom labels based on old node label by writing assigning rules For example rule Sealce 2km Sealce25km BrightnessTemperature gt Tb means to keep Sealcel2km as new label if the old label has Sealce12km to keep Sealce25km as new label if the old label has Sealce25km and to keep Tb as new label if the old label has BrightnessTemperature 30 File Edit View Select Layout Plugins Help Toots SRRA 8 4255 ot Karma B Cortot Pane Jt lo etworktASC posten Demo SCi Aopm graphsigraph matching seaice seaice 1 xmi am cea sas BOs S Node Attribute Bosse fidge Atirbute fromser Network Attrtste Browser w 200M Lame cate gt te Pan Figure 6 10 1 Choose Assign Short Label and then fill in the rewriting rule File Edt View Select Layout Plugins Help Toots By yy n BS oe Karma i B DO Demo SCiZ oom oraphs oran chene d ti So Sa BOs S Node Atibute Mosse Exige Attrbute Bronser Network Attroute Browser te SOOM Lesio cho te Fan Figure 6 10 2 The resulting graph with new labels 6 11 Graph Matching You can select them from the network panel and
8. Cancel Node Attribute Browser Edge Attribute Browser Network Attribute Browser 5 ZOOM Mida Figure 5 1 Click on Karma toolbar If you have not already edited the configuration file or wish to use different settings chose the connection method you want to use and configure its connection parameters Choosing Axis2 the ServiceURL in the Axis2 Config panel needs to be configured choosing Rabbitmq all parameters in the Rabiitmg config panel need to be configured 2 When you are satisfied with your configuration settings click the OK button and a new dialog window will appear which prompts you for the workflowID you can get it when you use NetKarma Adaptor to harvest provenance from log files see http d2i indiana edu provenance_netkarma O Cytoscape Des 2B QQQQ B GB pAs B cot Karma Control Panel ZA Tg Network VigMapper asil J gt Network No d Without Annotation Data Panel SORES g ro Node Attribute Browser Edge Attribute Browser Network Attribute Browser in POOLI Figure 5 2 Enter the workflow ID Enter the workflowID of the graph you want to retrieve and select whether you want the annotations included in the graph or not then press the OK button to continue 3 After the plugin has retrieved the Karma provenance XML you will be prompted to choose the name and location to store that XMLfile Gi cytoxcape Desktop New Sw QQQ Q e
9. Drag and Drop A node shape onto the network view An edge shape onto the source node then click on the target node Double click To add nodes and edges specified in SF format slg eq WasTriggeredBy WasDertvedFrom lt m Node Attribute Browser Network Attribute Browser Welcome to Cytoscape 23 0 Right click drag to ZOOM Middle click crag to PAN Figure 6 12 2 1 The sub graph 2 You can go back to the parent graph by clicking on the item in the network panel on the left hand side of the screen 37 O Cytoscape Desktop New Sess File Edit View Select Layout ea aaa ee she Karma HB Control Panel Tg Network yizMapper Ei gt pe 13 1 12 0 Figure 6 12 2 2 The parent graph 6 12 3 Compress Process Artifact Right clicking on any node in the graph you will see menu options for Compress Process and Compress Artifact Clicking on Compress Process the Cytoscape visualization plugin will eliminate all of the Process nodes that link to two artifact nodes with the outgoing edge represents the relationship used and the incoming edge represents the relationship wasGeneratedBy The process node will be replaced by a new oe between these two artifact nodes that represents the relationship wasDerivedFrom Larreren sneer BE AANA ob IEEE TEC Karma TI B mrg Drag and Drop Anode shap
10. EU E E A E A E E 31 012 Creanne an abstract VIEW st ere bee pense denentscesentecestweeceecactiesecuscatactacaadutusicnesnneceate eetesacemmmiaasohesnsboneane 34 Gs lustenne neit hbor Nodos snari te saccade sees EENET EERE EEEE REET 34 6 12 2 Navigate between graph and Sub graphs ee ececcccccccceececeecceceeeceececeeeeeeeeeaeeaeaaaeaaaaeaaaaags 37 6 123 Compress Process Agi AC ro ccatcenncecossenc scsascansenasincenssesecwss acsaetcncnannsantneesswonttetontoneseuendonceee 38 1 Introduction We have developed two plugins to Cytoscape to visualize and navigate provenance information contained in the NetKarma provenance system The NetKarma provenance retrieval plugin is used to retrieve provenance graphs from a remote NetKarma server to your local machine In the Cytoscape tool this plugin is run by clicking on the blue Karma icon in the Cytoscape tool bar after the plug in is installed The second plug in is the NetKarma visualization plug in which allows you to visualize and manipulate graphs downloaded using the retrieval plug in The NetKarma visualization plug in 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 ru
11. Enter time interval in milliseconds S Onang space te events 10 es O Figure 6 5 2 Configuring the time interval 6 6 Saving graph as XML To save the provenance displayed in Cytoscape as an XML file based on the Open Provenance Model OPM right click on any node and select the menu item Export OPM You 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 nitp openprovenance org File Edit View Select Layout Plugins Help Tools CIJELE JEL LEE Karma B Process 6 Visual Mapping Bypass Figure 6 6 1 Click on Export OPM 24 Fl Cytoscape Des SBa aA a ab D E Bp corms s TB Control Panel Tg Network vamoppe E mE Network No Ed a Figure 6 6 2 Choose the location to save the xml file 6 7 Get 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 utilizes a background communication with the Karma server Fle Edit View Select Layout Plugins Help Toots sajaa d a BANE od Karma T B Control Panai E fy oot Watapa Editor aters Network Nodes Gives l Node Atr ute Browser Edge Atybute Bowser Network atrbui
12. NetKarma Provenance Retrieval and Visualization Plugin For Cytoscape User Manual V1 3 0 Jan 30 2013 NetKarna Copyright 2013 The Trustees of Indiana University This document contains instructions for using the NetKarma provenance retrieval and visualization plugin version 1 3 0 which provides core capability to retrieve provenance information from a NetKarma 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 tu edu d2i provenance for more information Contents l 2 3 4 ay 6 Koheges UC a6 Pern err E eee nent erento none ner EE ee ee ee eee 4 SA eg Dey bled 100 cy te Lets ere nr eee en E eon eet er ee eT ee ee eee en ere eT 4 2 1 DCCC CG 1 INCI acc E T AA A A E E E A ET 4 22 PaaS Coe MAIO i dependence S eoor EEEE AO EEE E EENE NEEE EEE 5 IG CT VD T E E ATA A AE A A AAE ET TATT 5 3 1 Installing under Mac Linax Unix OS esas adsnicssascesnetiasebaazadastaiesheasinsetandoencdneesdeenvetaceaienneptsupeenosensdes 5 332 Installing under Windows OS oss s0 c0tssassavevaatseneaesteeaeboasdaceduavancdantandueunteneeecctece eateventioncedsensandoobnes 6 Co I
13. Panel SOs 8 Node Attribute Browser Edge Attroute Browser Network Attribute Browser Right click Grea to ZOOM Middle click drag to PAN Figure 6 2 2 1 Select the Network Simulator Layout algorithm 15 I Cytoscape Desktop New Sessio File Edit View Select Layout Plugins Help Tools E QQQQ 8 8 F455 B cow Karma BO Control Panel E Oo networleC Users peng Desktop Bloomington Dos GENI223 wimand network C Users per768 0 136 KAN AANA WAAAY Nii ANY ANY Data Panel RE Oave Node Atribute Browser ght click drag to ZOOM Middle click drag to PAN M 3 Windo Wi Karma 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 f O Cytoscape Desktop New Sessio File Edit View Select Layout Plugins Help Tools SARGE By Sy oot Karma Scale Control Panel Align and Distribute Tg Network Network tere yFiles GENI OPMLayout NS Layout Cyt
14. S NTN O T E E E E A 7 4 1 Updating the configuration files to connect NetKarma provenance retrieval and visualization pe me to Nek Aly SeN C eranen E E E aoausueeuiuieneat 7 4 2 Updating the configuration file for Karma visualization plUG1N ccccccccseesssesseeeeeeeeeeeeeeeennens 8 Using the Karma provenance retrieval plugin ee ccccecccceeeceeceeceeeeeeeeeeeaneaaeeaaeaeeeeeaeeeaeeaseeeeeeeeeeeeeees 8 Using the NetKarma visualization plugin oo ceecccccccccccceceececeecececeeeeeeeaaaeeaaaaaeeaaeeeeeeaeeeeeeseeeeeeeeeeeees 10 6 1 Load the Karma provenance XML file sssiciccccnesccatasssannonntencccetiescuacediodicbentionsenc saseedensddaseedeesusdsesee 10 6 2 Applying layout algorithms to the Karma provenance graph ssseseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 13 6 2 1 DEANS E E E EE E vee oa pees cote to ma E E T eaee 14 6 2 2 Network Simulator Mody OUT eissai E E EE E EEEE 15 6 2 3 Network Simulator Layout Extension TD vscscsnncssnccecndycncandasedencetensipbwnnpes a N i a 16 6 3 E VASA SOY Oa e E A E E NEE 21 6 4 Navigating the Karma provenance graph cececceccccccceeceeceecececeeeeceeceeceeeeeaeeaeeaaeeaeeaaaaaaaaaaaaas 22 6 5 PPV AY iN AOS bea set E AE E T AA EEE OAS A P A E N 23 6 6 Beh VIN E e y Y pape ence E A ATA E A 24 6 7 Gerdi POr nne SO ene E A E eee ee 25 6 8 Get data forward grapli seninem E a RE EEEE E EERE a ina enait 28 6 9 CCE Gs SOC TAU WOK HON IP aea E A E E 29 CHO An aS nOn abe oea E E E E N 30 OAE P
15. S Sy 435 B oon Karma la Control Panel mat ts Network VizMapper gt Data Panel BONE 8 iD f A Fie name test Network menwork Files of type sani files xmi Cancel Node Attribute Browser Edge Attribute Browser Network Attribute Browser 6 to ZOOM Midd m 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 reduce the time required For large provenance graphs we generally 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 is retrieved successfully Please be patient while waiting for a graph to be downloaded 6 Using the NetKarma visualization plugin 6 1 Load the Karma provenance XML file 1 Click on the GENI toolbar 10 Cytoscape Desktop iNew seas SH QQqgna ese gD A y Ay EF cont Karma Control Panel ral OPM Visulization Plugin tool ti fe Network yizMapper gt Network No Ed gt gt Import an OPM Graph from xmi fie mth nnotaton Axis2 Config Rabbitma config Data Pane fd Ov o Ov oO ID Current Session al network attributes wil b
16. ape 2 8 0 Figure 6 2 3 5 Set the mapping type to Passthrough Mapper 18 Figure 6 2 3 6 Graph with customized node graphics showing the statistic of packets been dropped and sent No Cytoscape Desktop File Edit View Select Layout Plugins Help Tools fo 2 22 E E Karma BL say ire i 6 2 3 7 Customized node apie 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 oraph url queuing amp transfer f o Ao ry B QQQ0 Q 8 8 8533 o Karma TB Control Panel ot Oc File Edit View Select Layout Plugins Help Tools 2B QQ0Q 8 8 B4y 55 Boot Karma BL Edge Target Arrow Sh interaction Node Visual Mapping Node Color NodeType Node Custom Graphics 1 graph url queuingStransfer Mapping Type Passthrough Mapping File_475 on tinuous Mapper File_474 pessmwengh Mapper File_473 File _472 File_S39 File_471 File_123 File_122 click drag to ZOOM Middle click drag to PAN Figure 6 2 3 9 Set the mapping type to Passthrough Mapper 20 6 Ctoscane Deskin File Edit View Select Layout Plugins Help Tools buana a E ake Karma MHB Editor Fiters Figure 6 2
17. choose the algorithm for computing the Discrete Classification of Node Attendance Basically for each of the node in the first graph the algorithm tries 31 to find a most matched node in the second graph The matched nodes are not identical but they will be similar in node attributes neighbor node attributes connecting edge attributes and node topology Besides matching subgraphs will be calculated and assigned with the same colored If you click on any of the node in the first graph the matched node in the second graph will be highlighted and the attribute panel of both nodes will be displayed side by side File Edt View Select Layout Pluges Help Tools G18 2 2 A e 9 B39 Fy o karma TEB Le networkEASC poster Demo SC12 opm graphs graph matching seaice seaice 1 xml bom vetapper Eat ers Node Atr bute Bose Sigs aos eas OS asa seas Melcome te Ctoetepe IEI ic v oou Missio cti o w PAN Figure 6 11 1 Select two graphs from the network panel and choose DCA comparison File Edt View Select Layout Plugins Help Toot 1S 22 Oleh DATAE ey karma __T B lt networkE SC poster Demo SC12 opm graphs graph matching seaice seaice2 xmi BokEe EEEE toge ti irons Nemort Atrrbute Browser te ZOOM tneaie cne grag te PAN Figure 6 11 2 Graph matching result One matching sub graph is found and colored in red 32 o Cytoscape Desktop New Session Om Fi
18. ck on node 4 Clustering the neighbors of the node selected in step 3 Cytoscape Desktop New File Edit View Select Layout Plugins Help Tools amp B QQ0 Q 6 8 8 4955 o Karma BS On empty space to create 8 node On a node to begin an edge and specify the source node Then cick on the target node to WosTriggeredBy WasDerivedFrom Gln node attrbute Browser Edge APEU Browser Network Attribute Browser Welcome to Cytoscape 28 0 Right click drag to ZOOM Middle click drag to PAN Figure 6 12 1 5 Cluster nodes 5 Repeat step 4 until you got an abstract graph showing only the smaller set of nodes you wish to visualize 36 3 erp ee Cytoscape Di File Edit View Select Layout SERRAR D BRB ei Karma BB seu f Network are Editor gt Instructions Drag and Drop A node shape onto the network view An edge shape onto the source node then cick on the target node To add nodes and edges specified in Figure 6 12 1 6 Create abstract graph 6 12 2 Navigate between graph and sub graphs Once you have created an abstract view you can navigate between that parent abstract view and the sub graph for any collapsed node 1 ze Desktop PERU click on any abstract node will show the view of the collapsed sub graph RV Cytoscape Desktop hk File Edit View Select Layout Plugins Help Toots SERAQ DD By Boot Karma sex fi F
19. e Browser Welcome to Cytcecece I8 2 Right chct o te DOOM Ahosie ctice Gag 1 FAN Figure 6 7 1 Get data provenance history 25 File Edt View Select Layout Plugins Help Tools 2B Q2QQQ B 8 B4y 33 o Karma lt BB HE AST Data Panes B0 8 Node Attribute Browser Edge Attribute Browser Network Attibute Browser Welcome to Cytescepe 282 Ragrtclice asg ts ZOON Micsie clice drag to PAN Figure 6 7 2 Initial return graph is in Attribute Group Layout and you can change it to other layouts File Edt View Select Leyout Plugins Help Tools EB AQ08 BOB Fy 33 oi Karma OOOO T B ConmeiPanes FRR ASST provenance eee ereee N ERA Welcome tz 282 3 ZOOM Ahosteciica e to PAN Figure 6 7 3 Provenance history graph refined from Force directed Layout Since force directed layout do not avoid crossing edges most time you need to manually move clusters around to avoid them To solve this we developed customized layout Fast Provenance History Layout and Force Refined Provenance Layout 26 Cytoscape Desktop New Session Edit View Plugins Help Tools eukana 6 By 3 oe Karma T B 5 networkE SC poster Demo SC12 opm graphs Provenance history and forward provenance provenance history xm eee Network New Ee GORS goe So we se Uva amp E Node Attribute Browser Edge Attribute Browser Network Attribute Browser Welcome
20. e Edt Vies Select Layout Plugins Help Tools ea ELLE Agin o Karma we jedi ee la Se TT Be Network E SC poster Demo SC12 opm graphs graph matching seaice seaice2xmi S088 8 5em Node Atrtute Browser Edge Atybute Bowser Network AtrOute Browser Welcome te Cricscepe 282 Raght ches asg to ZOOM Ahocte chcs Gag t Pan Figure 6 11 3 If you click on an unmatched node a message no matching graph will be promted o Cytoscape Desktop New Session Oma Fie Ede Vies Select Layout Phugins Help Toots Saaga a g By o Karma O BORE a mepa Edge Anrrbute Browser Network Atybute Browser Welcome te Crtmecope IAI v TOOM Marie tics PAN Figure 6 1 1 4 If you click on a matched node the corresponding matching node and their attribute panels will be displayed for comparison 33 6 12 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 NetKarma visualization plug in that can be sued to abstract out some of this complexity to allow you to visualize specific aspects of the provenance graph 6 12 1 Clustering neighbor nodes To deal with graphs with a large number of artifact nodes the NetKarma visualization plugin supports extracting an abstract view by clustering neighboring nodes As an example Figure 6 8 1 1 shows a graph that has a larger number of artifact
21. e lost Do you want to continue OK Cancel Caine Attrbuite Drauear Minhenski Attu ite Orauear Figure 6 1 1 Click on the GENI toolbar Select whether to import the provenance xml with annotations or without annotations When you import 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 you select any node in the provenance graph during navigation the Karma visualization will retrieve more information for it 2 If you choose to import provenance without annotations you also need to choose which connection method you want to use for the background connection and configure the connection parameters WF Cytoscape De Ktop New Se 2B QQQQ o 8 4y 45 ot Karma Control Panel ral t Network VizMapper No Ed gt gt Import an OPM Graph from xmi file withAnnotaton withoutAnnotation Aus2 4 Rabbetmg Axis2 Config Rabbitmg config username quest password guest hostname 156 56 5 233 Panel Data Pane hostport 5672 Lj BY virtualhost ID exchangename KarmsExchange Quevename KarmaQueue routingkey KarmakKey Current Session al network attributes wil be lost Do you want to continue OK Cancel tribute Browser Edge Attribute Browser Network Attribute Browser ag to ZOOM Micdle click ora J Figure 6 1 2 Configure the connecti
22. e onto the network view An edge shape onto the source node then click on the target node Double click To add nodes and edges specified in SIF format CTRL click On empty space to create a node On a node to begin an edge and specify the source node Then cick on the target node to finish the edge Speofy Identifier wasGeneratedBy Te 6 12 3 1 A provenance graph before applying Compress Process 38 E Aer 2p AAEN A ee ee l EE E Karma pe Ea a Drag and Drop A node shape onto the network view An edge shape onto the source node then click on the target node Double click To add nodes and edges specified in SIF format CTRL click node21 On empty space to create a node Visual Mapping Bypass gt On a node to begin an Nested Network riii Use Web Services gt source node Then cick on the target node to Hide Node finish the edge LinkO R Data Provenance History Spedfy Identifier Load Detail Info Compress Processes e E Compress Artifacts Export OPM wasControledBy NEN eae Cluster Neighbors sat ats 2 Play Mo s gt a I MOas Heo D wasDerivedFrom 4 Scalia node atrovte Bronzer EGE ARBRE Bronse Nebo ARB rovae Welcome to Cytoscape 28 0 Figure 6 12 3 2 Applying Compress Process Cytoscape Desk lacbion pa File Edit View Select La
23. guration files will be loaded at the startup of either plugin and the configuration settings will be displayed in the configuration panel You can choose which option you want to use in the configuration panel and modify the default configuration settings The modifications will be saved back to the configuration files automatically Besides making configuration changes through the configuration panel in Cytoscape you can directly modify the contents in the configuration file and the file karmaQueryConfig txt has the same configuration entries as the file karmaVisConfig txt To set up the configuration for connecting via the Axis2 webservice There is only one property the needs to be set when using the Axis2 server axis2 serviceURL enter the URL to the Karma To 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 how to label nodes Different from our previous version this version of NetKarma visualization plugin will import all the annotations into Cytoscape graph as attributes However you can still choose the label of nodes from one
24. ight click drag to ZOOM Middle click drag to PAN Figure 6 2 1 1 Select the X sort algorithm 14 Cytoscape Desktop New Session File Edit View Select Layout Plugins Help Tools E QQO G B 8g 35 Boo Karma B Anode shape onto the network view An edge shape onto the source node then click on the target node Double click To add nodes and edges specified in SF format CTRL click On empty space to create a node on the target node to finish the edge Specify Identifier WasGeneratedBy A WasTriggered8y WasDerivedFrom Node Attribute Browser Edge Attribute Browser Network Attribute Browser Welcome to 280 ick to ZOOM Middle click to PAN 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 1f 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 E Cyto cape Desktop New Sessic File Edit View Select Layout Plugins Help Tools ve By by e Karma T B Data
25. ns quantitatively and to do model selection with an effective collaboration between the user and the discovery system Karma is a standalone system that can be added to existing cyberinfrastructure for purposes of collection and representation of provenance data The NetKarma 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 NetKarma plug ins retrieve provenance as graphs from the NetKarma provenance server To use the Cytoscape plug ins you will need to either setup a NetKarma server or process a log file using an established NetKarma service such the 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 1u edu d2
26. on to Karma Server 11 4 pA a mwa Se QQgagnge EN o a S Sg B con Karma Control Panel SA Network VizMapper Editor aj Instructions Drag and Drop Double click CTRL click Specify Identifier Add an Edge Add a Node Add 4 Nested Network Veicome to Cytoscape 2 8 0 Right click drag to ZOOM Middle click drag to PA Sw aaa By ry oei Karma E Control Panel S ss network C Users peng Desktop Graph_opmami ts_ gt ES fe Network VizMapper Editor Instructions Drag and Drop Double click CTRL click Specify Identifier Add an Edge Add a Node Add a Nested Network ome to Cytoscape 2 6 0 Right click drag to ZOOM Middle click drag to PAN A node shape onto the network View An edge shape onto the source node then cick on the target node Look in Graph_opm xmi 2 rB Lami T O new_out3 xml new _out5xmi Recent Items new_out xmi To s d nodes and edges O tm_outlami specified in SF format tm_cut2 xm ts_out2xmi ts_out3 xmi On empty space to create anode Data Panel On a node to begin an edge and specify the fe aad gy g 5 D Hee source node Then cick on the target node to firesh the edge E i File name ts_out4 xmi Qper Network Fies of type sand files xmi Cancel O
27. oscape Layouts OPM X sort JGraph Layouts NS Layout Extl J ClockwiseAttributeCircleLayout gt Settings al Data Panel peg Lj Ov o Ov o ni aian Edge Attribute Browser Network Attribute Browser ghi click drag to ZOOM Middle click drag to PAN Figure 6 2 3 1 Select the Network Simulator Layout Extension 1 16 Figure 6 2 3 2 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 3 toscape Desktop New Session File Edit View Select Layout Plugins Help Tools DD BE o Karma B ad Midcle click drag to PAN Figure 6 2 3 3 Add the Node Customized Graphics visual mapping 17 To show the statistics on dropped amp sent packets user can map the graphics to graph url drop amp sent A Cytoscap e Desktop New Session r 4 meee ree cures Karma BL ConmrotPanet AT File Edit View Select Layout Plugins Help Tools B QQ0Q 8 8 8 335 Boot Karma BS E Edge Target Arrow Sh interaction 1 Node Visual Mapping Node Color NodeType Node Custom Graphics 1 graph url drop8send Mapping Type File_475 File_474 an iia a Fie_473 Fie_472 a SOV 8 fo amp Fie_471 File_123 File_122 Welcome to Cytose
28. r Network Attribute Browser Welcome to oap ght click d g to ZOOM Middie click drag to PAN Figure 6 4 1 Double click on node 2 Double click on any edge to see its attributes 22 Ko Cyto ape D merae SERRARA NER Karma TB poe fl fin h at Jul EEEN Figure 6 4 2 Double click on edge 6 5 Playing movie If you right click on any node you can choose to play a movie displaying the provenance for that node based on the order of the timestep or time attributes of the nodes Ko Cytoscape Des Yew Sess File Edit View Select Layout Plugins Help Tools 2E QQ0Q 6 8 83453 Rov Karma T fg Network vigMapper Editor Process_17 Visual Mapping Bypass Nested Network Use Web Services Hide Node LinkOut Data Provenance History Load Detail Info C ress Processes Panel na Data Compress Artifacts Ov o Ovo a Export OPM Cluster Neighbors Play Movie _ Node Attribute Browser Edge Atribute Browser Network Attribute Browser clicks drag to ZOOM _ sMidcle click Grag to PAN Figure 6 5 1 Display provenance as a movie You can also configure the time interval on milliseconds between the appearances of two nodes in the movie 23 ES Cytoscane D Fenetre Selertitayouti Paginas tidien ep acne gs Bako Karma T B a Drag and Drop A node shape onto the network view specified in SF a e
29. ram files cytoscape 2 8 1 plugins 4 Copy the configuration files into the plugins directory under Cytoscape_v2 8 1 Create a new directory named config under cytoscape s plugins directory mkdir C Program files cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma visualization plugin copy visualization OPM_visualization config C Program files cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma provenance retrieval plugin copy visualization Karma_query config C Program files cytoscape 2 8 1 plugins config 5 After you finish installing the two plugins the plugins directory under Cytoscape_v2 8 1 will look like Cytoscape_v2 8 1 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval jar config karmaQueryConfig txt karma VisConfig txt pluginConfig xml 4 1 Updating the configuration files to connect NetKarma provenance retrieval and visualization plugins to NetKarma service The following describes how to configure the provenance retrieval and visualization plugins and connect them to a running Karma service You have two options Axis2 webservice or RabbitMQ messaging system to connect to a Karma server and all of the configuration information is stored in the file karmaQueryConfig txt for NetKarma Retrieval plugin and in the file karmaQueryConfig txt for NetKarma visualization plugin Those confi
30. rectory of OPM_visualization type in the command ant If succeed a jar file named KarmaGraph jar should be generated To build the NetKarma retrieval plugin you need to edit the file visualization Karma_query build properties lt Define the Cytoscape directories gt cytoscape dir C Program Files Cytoscape_v2 8 1 the directory where Cytoscape is installed on your computer In the directory of Karma_query type in the command ant If succeed a jar file named KarmaRetrieval jar should be generated 3 Copy the jar files into the plugins directory under Cytoscape_v2 8 1 Deploy the NetKarma visualization plugin cp visualization OPM_visualization KarmaGraph jar cytoscape 2 8 1 plugins Deploy the dependent libraries for NetKarma visualization plugin cp visualization OPM_visualization lib cytoscape 2 8 1 plugins Deploy the NetKarma provenance retrieval plugin cp visualization Karma_query KarmaRetrieval jar cytoscape 2 8 1 plugins Deploy the dependent libraries for NetKarma provenance retrieval plugin cp visualization Karma_query lib cytoscape 2 8 1 plugins Note some libraries are shared by NetKarma visualization plugin 4 Copy the configuration files into the plugins directory under Cytoscape_v2 8 1 Create a new directory named config under cytoscape s plugins directory mkdir cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKa
31. rma visualization plugin cp visualization OPM_visualization config cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma provenance retrieval plugin cp visualization Karma_query config cytoscape 2 8 1 plugins config 5 After you finish installing the two plugins the plugins directory under Cytoscape_v2 8 1 should look like Cytoscape_v2 8 1 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval jar config karmaQueryConfig txt karmaVisConfig txt pluginConfig xml 3 2 Installing under Windows 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 Same as step 2 in Section 3 1 3 Copy the jar files into the plugins directory under Cytoscape_v2 8 1 Install the NetKarma visualization plugin copy visualization OPM_visualization KarmaGraph jar C Program files cytoscape 2 8 1 plugins Deploy the dependent libraries for NetKarma visualization plugin 6 copy visualization OPM_visualization lib C Program files cytoscape 2 8 1 plugins Deploy the NetKarma provenance retrieval plugin copy visualization Karma_query KarmaRetrieval jar C Program files cytoscape 2 8 1 plugins Deploy the dependent libraries for NetKarma provenance retrieval plugin copy visualization Karma_query lib C Prog
32. to Cytoscape 28 2 Right click drag to ZOOM Middle click drag to PAN Figure 6 7 4 Provenance history graph refined from Fast Provenance History Layout You can find the layout algorithm from Layout Geni OPM Fast Provenance History Layout and then apply force directed layout to tangled clusters as you want The problem with this layout is that you cannot judge the number of nodes inside each cluster based on its size We solve this by Force Refined Provenance History Layout e Cytoscape Desktop New Session 0 EJ File Edit View Select Layout Plugins Help Tools BE 2ane 68 By GEC Karma B Co HI networkEA SC poster Demo C12 opm araphs Provenance history and forward provenance provenance history xml 1 Neto oper eo eel fe Lj Ova amp Ov o oS i Node Attribute Browser Edge Attribute Browser Network Attribute Browser i Welcome to Cytoscape 28 2 Right click drag to ZOOM Middle click drag to PAN Figure 6 7 5 Provenance history graph refined from Force Refined Provenance History Layout You can find the layout algorithm from Layout Geni OPM Force Refined Provenance History Layout and then apply force directed layout to tangled clusters as you want 27 Note The query functionality works best when the Karma visualization plugin is connected to Karma using Axis2 webservice instead of the RabbitMQ 6 8 Get data forward graph Right clicking on any artifact
33. will display an option for Data Forward Graph Selecting that option will display the data forward graph with all the future data products that are derived from the selected artifact File Edt View Select Layout Plugins Help Tools 2A QQ 8 B4y5 1 o Karma BB ConteiPamet TD Ta emort uistapper Banor Fines tenon Nodes Eager Data Pane BOs 8 Node Attribute Browser Edge Attrbute Browser Network Attribute Browser Welcome is Cyptescepe 282 mgran sog v DOOM Lhase cios meg i Pan Figure 6 7 1 Get data forward graph 28 File Edt View Select Layout Plugins Help Tools PEAanaled a Dhyhow Karma OOOO T B Te retort mellan etso o eo Petcare ta Cytascspe 2 2 bd te 2004 Mistiochce ran Figure 6 7 2 Data forward graph The right up corner is the beginning of the tracing graph 6 9 Get associated workflow graph If you want to view the provenance graph that is responsible for generating a data product you can right click on that data product and select get associated workflow graph File Edit View Select Layout Plugins Help Tools jeaeane 2 8 BAB Karma S __ B p Data Panel o SOKE 8 D Node Atribute Browser Edge Attrbvte Browser Network Attribute Browser Welcome to Cytoscspe 2 82 a 1 n a Figure 6 9 1 Get the associated workflow graph for an artifact in data forward graph 29 File Edit View Select Layout Plugins Help Toot amp BQ
34. yout Plugins Help Tools eee SS e A E Karma TB we j nose Attribute Browser Edge AtB Bronzer Nebrork Aut Browser click desg to ZOOM Middle click drag to PAN Figure 6 12 3 3 The provenance graph after applying Compress Process Clicking on Compress Artifact the Cytoscape visualization plugin 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 39 fz Cytoscape Desk op New S File Edit View Select Layout Plugins Help Tools 2E QQQQ g BS By hy Boot Karma Fle Ect View Select Layout Plugins Help Toots Laaa aD ahha Karma TFB node21 Visual Mapping Bypass Nested Network Use Web Services i tee Node LinkOut Data Provenance History Load Detail Info Compress Processes Figure 6 12 3 5 Applying Compress Artifact 40 lt O Cytozcape Dekon New S lel ola To add nodes and edges specified in SIF format CTRL click On empty space to create a node On a node to begin an edge and specify the source node Then cick on the target node to finish the edge 41
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