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FCModeler User`s Manual

1. Create Info When users open a new data file the View Info button will become Create Info Users can create new experiment information Seles Change Color Color Selection High Value ES Middle Value FI Change Color Low Value a Change Color UK Preview Color Bar 12 w d4 w 16 iw 20 W 38 Animation Control Panel d led File Data Type Data analysis Input Data Select Data File View Profiles scaled Expression Value Time hour Double click to highlight b TI T1G10670 Standardize Profiles Reset UF amp T1G361 Profile AT 163158430 at sample point At Starch S D1 wi 0 SLE is selected Figure 35 View Profiles dialog 12 3 5 Data preprocessing details used in animation R In order to visualize and interpret the data more effectively the data 1s preprocessed e Trim the outliers It is very possible there are outliers which will skew the color mapping Here we trim expression value over 98 of the global maximum expression value and less than 2 of the global minimum expression value e Linearly scale the trimmed expression values to the range 0 1 The 1 value corresponds to the high value color 0 5 value corresponds to the median value color for fold change data 0 5 value corresponds to no change and the 0 corresponds to the low value color 12 4 Write your own R script The example script animation R is located in the f
2. all of the nodes of H must be in D all of the edges of H must be in D and the edges of H must have both end nodes in H For a given digraph D V E a subdigraph H can be created in several ways e Given a set of nodes W c V D o V H W o E H v u e E D v u V H o H consists of some subset of nodes of D and all edges in D with both end nodes in that set e Given a set of nodes W c V D and an integer p o V H NDW o E H v u e E D v u V H o NPI W is defined as the closed p th neighborhood of W Saving W and all nodes visited on directed paths of length p from each node in W forms the set o Nibw wr wU nar bv Un WUN Gv i 0 p l i Niro wi wi n D NS v and N W is defined similarly i 0 e Given a set of edges B c E D o V H veV D v e v u e E H o E H B o H consists of all end nodes of the edges in B and all of the edges in B e Given a set of nodes W c V D and a set of edges B c E D o V H W o E H Kv u e Biv u V H o H consists of all nodes in W and all edges in B with both end nodes in W 11 2 Strongly Connected Components A digraph D is strongly connected if every vertex of D 1s reachable from every other vertex of D The strongly connected components SCC s of a digraph D are the maximal strongly connected subdigraphs of D The SCC s are useful to analyze because every node in an SCC s reachable from every other node in the same SCC 32 The alg
3. the graph archive FCModeler will display all available information including information from the topology index pathway and extended files If reference information 1s available web links may be shown in the panel which will open your web browser when clicked 20 A FCModeler ATIG16350 File View Layout Graph Interaction Modify Tools Window GQBaaeBoe x ATIG79470 ATIGI6350 ATIG79470 GUANOSINE Pi Pi r Node Table nodeName nodeType location id SS XANTHOSINE 5 Pi D reaction Enzymatic reaction unknown 17557 AT1G16350 p _ cytosol 8312 Ei AT1G16350 i unknown 191 2 unknown h 121 7 unknown 845 0 unknown 849 0 unknown 644 unknown 1121 6 dt 1240 2 unknown 17696 head directed edgeType strength 1 certainty id AS pa st m Rn X De rue Translation GUANOSINE reaction true Enzymatic 1 reaction GMP rue Enzymatic 11 direct evid ATP reaction frue Enzymstic DD directevid H20 reaction rue Enzymatic 11 direct evid eu NAD reaction frue lEnzymatio DD directevid 845 0 176 H20 reaction rue Enzymatic direct evid 1121 6 17 reaction NADH true Enzymatic _ direct evid 17698 84 GIN reaction fe Enzymatic drec
4. Edges button in the Modify Edges dialog A message box will appear asking you to confirm that you wish to delete the selected edge s If you click OK they will be permanently removed from the visible graph and the archive the edges will no longer appear in any subgraph Deleting an edge can not be undone 5 4 Moving Nodes and Edges Nodes can be moved by selecting them and dragging them with the mouse Attached edges will move with the selected nodes Edges can be moved by selecting the edge then manipulating the control points which are shown as blue boxes see Figure 10 The node and edge positions can be saved in a coordinate file for reloading otherwise they will be lost whenever a layout is applied or if the graph is closed 17 Fu FCHodeler EMEN Log f View Lavo Graph Interaction Mod y Tools Window _ Figure 10 Selected QE AAD BO J edge showing control al icheyenneleclipse emodeleribinigraphsieyeieTest zip points 5 5 Zooming FCModeler supports zooming of the graph view to examine the graph in varying levels of detail To enlarge the graph select View then Zoom In from the top menus or click the amp toolbar button To zoom out either select View then Zoom Out from the top menu or click the amp toolbar button 5 6 Finding a Particular Node In very large graphs it can be difficult to locate specific nodes Nodes can be searched by using the Find Node dialog Figure 11 This dialog will let you find a
5. Enzymatic reaction vl I 3 mi vis equal to Then line color v is E3 blue vl Add Mapping Rule Mapping Rules Load Mapping File view Default Mapping Delete Selected Rule Delete All Rules edgeType Enzymatic reaction maps to line color z BLUE E ATSGOIEN 1 x I shp M matwit Cod Pimele acid Co4 cost Ns wdi 4T3G57390 edic acid ING ao Manual Entr AN A mort T og 5 Ma 2 13 A S SUN i aN 7 TU LL i E Y gt lt ill M EX IM FA N u i m A VISE UT y t fyi Figure 16 The Mapping Editor after creating one mapping rule based on edge properties 8 1 Using the Node Properties and Edge Properties tabs The particular nodes and edges to be altered can be selected based on their properties For example consider a graph that has several types of nodes and edges such as the one shown in Figure 16 Suppose we want to color all edges of type enzymatic reaction blue To do this we click on the Edge Properties tab and create the mapping rule If edgeType is equal to Enzymatic reaction Then line color is blue as shown in Figure 16 Click the Apply button to view the effect the mapping rule has on the graph while leaving the Mapping Editor open To change the appearance of all nodes with
6. Line Mappines Node Properties Edge Properties Pathway Selection If certainty v jis equal to indirect evidence edgeType vis equal to Catalysis is rea Add Mapping Rule Then line color Figure 17 Mapping editor configured to create the compound mapping rule If certainty is equal to max amp Node and Line Mappings Node Properties Edge Properties Pathway Selection If nodeName NY is equal ta ADP vi v vj Add Mapping Rule wlis equal to xi is N other Then node fill color Figure 18 Mapping editor configured to create the mapping rule If nodeName is equal to ADP then node indirect evidence or edgeType is equal to Catalysis then fill color is light blue line color is red 8 2 Using the Selection tab The Selection tab of the Mapping Editor Figure 20 allows mapping rules to be created for the nodes and or edges that are selected 1n the graph First select nodes and or edges in the graph then click the Get Selected Nodes and Edges button The number of nodes and edges selected will be displayed in the label to the Edges button left of the Get Selected Nodes and After the nodes and edges have been selected using either method you can indicate the desired appearance of the selected objects The same attributes are changed in the same vvay as on the Node and Edge Properties tabs By default FCModeler w ll make mapping rules for both the nodes and edges If
7. adjacent nodes AGEM gives a layout that is similar to the regular GEM but does it much faster Because of the lack of repulsion between nodes an unlucky initial random layout could leave many nodes bunched together Also the reversed gravity tends to push singletons and disconnected subgraphs away from the barycenter This increases the global temperature of the layout causing it to use its maximum allowed number of iterations instead of stopping early due to settling of the graph 12 4 3 3 FastGEM FastGEM is a compromise designed to give the more consistent quality of GEM while retaining some of the speed of AGEM FastGEM uses AGEM to do an initial layout and GEM to finish AGEM replaces Frick s insertion loop With a layout that is often near to the final layout the regular GEM algorithm runs significantly faster If there are disconnected pieces of the graph the AGEM algorithm will take a long time to complete so any speed advantages over GEM will be lost 5 Interacting with the Graph View 5 1 Selecting Nodes and Edges Multiple nodes and or edges can be selected at any given time as shown in Table 1 Selected nodes and edges are highlighted in the graph nodes by a yellow border and edges by a thick red line Table 1 Methods of selecting nodes and edges To Select Do This Action Individual node or edge click on a node or edge Multiple nodes and or edges hold the Ctr1 key and click on multiple nodes and or edges Multip
8. by the animation R R script file Do not change any settings but click the OK button the Show Animation dialog Figure 28 should appear so you can view the data in the context of the metabolic and regulatory map 12 3 Use of the Animation Control Panel The Animation Control Panel dialog is used to view and modify the data the animation is based on We plan to have several additional functions available soon including the ability to 36 open multiple files For example you may wish to view proteomic data together vvith microarray data Also we want to add GUIs for data processing clustering and mapping to FCModeler 12 3 1 Input Data frame Select a microarray proteomic or metabolomic data file Select an Experiment Information File describing your experimental samples RNA protein or metabolites and how they were obtained For the data formats please refer to the example at the end of the document section 14 Appendix R Script File Formats 12 3 2 Data Preprocessing Setting frame This frame is used to select subset of the data Usually there are multiple replicates genotypes time points or treatments in a data file user can select specific subgroups of them as shown in Figure 34 Checking the Fold Change between GenoType box will show the fold change between different genotypes WT and mutant in the example data Checking the Average Replicates box will show the average expression of the replicates The Scale of Expre
9. name is selected on the main Subgraph Creator screen the dialog will change to look like Figure 23 All of the pathways will be listed in the large box select the pathway s whose nodes and edges you want included in the subgraph As many pathways as desired can be selected 9 4 Creating a Subgraph by P Neighborhood A p neighborhood is the set of nodes p steps from the node s of interest Nodes connected by an edge are one step apart For example the graph in Figure 25 shows the nodes that are one red and three green steps from AT3G58610 yellow The screen used to make p neighborhood subgraphs is shown in Figure 24 The example in Figure 25 shows the p neighborhood of one node but p neighborhoods can be made for many nodes The nodes that will be used for the p neighborhood subgraph are shown in the white list on the p neighborhood subgraph screen Nodes are added to this list by clicking the Identify Nodes each node selected using the Identify Node dialog Named Pathway Current Selection in Graph the node s selected in the top graph are added to the list or Read from File the file should be a simple text file listing the unique ID of each node on a separate line buttons After adding the desired node s to the list type the p value in the P box 27 E Subgraph Creator E Subgraph Creator BAX The new subgraph will be made containing all nodes within P steps of the indicated nodes Edges connecting the nodes will be included i
10. of rules can later be loaded by clicking the Load Mapping File button Saving and loading mapping rule files allows the appearance of a graph to be quickly altered without creating mapping rules each time Many mapping files can be created for each graph but only one can be displayed at a time 8 5 Advanced Mapping Rule Manipulation Mapping rules are managed with the buttons in the Mapping Rules frame at the bottom of the mapping editor All active mapping rules are listed in the large box An individual rule can be deleted by clicking on the rule to highlight it then clicking the Delete Selected Rule button all rules can be deleted with the Delete All Rules button If no default mapping file 1s set in the main FCModeler preferences clicking Delete All Rules then Apply will have the same effect as clicking the Revert button Mapping rules are applied in the order in which they are listed in the mapping editor list box top first bottom last The order in which the rules are applied may affect the appearance of the graph For example one rule such as If certainty is equal to high then line color is blue will change all edges with high certainty to blue Another rule such as If edgeType is equal to biochemical reaction then line color is red will change some edges to red Some edges may be both of high certainty and the type biochemical reaction If the first rule is applied before the second lines that are both high and biochemical reaction w
11. one visible on the screen in all the subgraphs or all of the information in FCModeler s memory regardless of whether it is visible or not The Contents file information frame lets you set general information about the data in the graph f you vvish When finished click the Save button on this screen which will make a standard file selection dialog appear in which the location and name to save the new archive can be specified Jb Save Graph to Graph Archive mas Modes and Edges to Save Q active graph window nodes and edges in top visible subgraph only Other Information to Save e information far nodes and edges to be saved only Q all information in memory Contents file information Date created Project hame Data source MetNet database vi Institution lowa State University koj Arabidopsis pathway information only Description Figure 1 Save graph option dialog This dialog lets you save information about the graph and to specify which part of the graph information to save 3 3 3 Saving an Image of the Graph FCModeler can create an image file JPEG SVG or PNG format of the displayed graph This may be useful for including the graph in a document or web page The entire active graph not just the portion of it visible on the screen if it is zoomed is included in the image and it is saved with the visible color and shape properties To create an image of the graph view select the Save Graph Image menu item from
12. side has three frames The boxes checked on the left side of the screen determine what is put in the list on the right side The right side lists node identifiers which identifiers are included is set by the left side boxes The Identify Node dialog will have different amounts of information depending on the files present in the graph archive For example Figure 12 shows the Identify Node dialog when a small graph that only contains a topology file is loaded The graph in Figure 13 has an index and pathway file so the Pathways frame contains items and the Properties frame has asynonyms entry By default when the Identify Node dialog is opened it lists the names of all nodes in the graph This state is shown in Figure 13 the node names option in the Properties frame is checked all rows in the Locations frame are checked and all rows in the Pathways frame are checked You can restrict the list of nodes to certain pathways and or locations by unchecking the corresponding boxes in the Locations and Pathways frames Additionally you can view nodes by type synonym or molecule ID in addition to name Click the Update View button after checking or unchecking boxes on the left side of the dialog to update the node list Nodes are identified by selecting their identifiers in the list on the right side and clicking the OK button You may select as many nodes in the list as you wish hold the Ct r1 key while clicking to select multiple entries or the Sh
13. 010 Click OK in the dialogs to close them e In Linux users can follow similar steps except setting the R HOME environment variable e The R functions have not been tested on Macintoshes For now please use a Linux or Windows environment on your Mac and follow instructions above 12 2 View Expression Data and Test the Configuration To test the connection open the SPathways zip graph archive one of the sample graphs that came with FCModeler Then open the Animation Control Panel by selecting Interaction then View Animation from Script from the top menu A file open dialog will appear from which you can select an R script to view Several test files are included with the FCModeler distribution select animation R The Animation Control Panel Figure 34 should then open Please check the background of the desktop if the GUI does not pop up This dialog is used to send information to R You can set what kind of node or edge properties are sent to R and filter the nodes or edges by properties pathways or selection Click the Run Script button and FCModeler will send information to R and run the selected R script Ifthe Animation Control Panel does not appear check if R is running and if R has the two necessary packages tkrplot and XML installed It may be helpful to close FCModeler and R including any R processes that might be running restart FCModeler and try again Figure 34 top left corner shows the Animation Control Panel produced
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15. 4 Write your owim R series t 39 2A da E ee eine 40 12 42 RE VAU Shan nn e e as eiUE 40 13 E E E E aie 41 13 1 Publications relating to FCModeler 00000000 ss eee enen eee eee 41 13 2 Open source Code Dsed un FE M deler nun er 41 14 Appendix R Scnpt FieFomalsaes ses ae 41 ELI Mieroamay DA Apnea 41 142 Other Dita en al ae he 42 14 3 Experiment information file format an example sse 42 1 Introduction to FCModeler FCModeler models and visualizes metabolic networks as graphs Nodes of the graph represent specific biochemicals such as proteins RNA and small molecules or stimuli such as light heat or nutrients Edges of the graph capture regulatory and metabolic relationships found in biological systems FCModeler can dynamically display user specified graphs and animate the results of different modeling algorithms on the graph The fuzzy cognitive map modeling software is currently written in Matlab and interfaces vvith FCModeler via xml graph files We plan to translate this software at a later date 2 KCModeler Installation The FCModeler distribution is compatible w th Windows 2000 XP and Linux machines Download the file and unzip into your directory This version is already compiled and the Java source code is included If you make any improvements to the code please send the updated modules back for inclusion in the next distribution FCModeler requires the installati
16. CModeler menu 5 3 1 Modifying Edge Information Information for a single edge can be modified using the Modify Edges dialog Figure 8 Select the edge whose information you want to modify in the graph then click the Get Edge button on the Modify Edges dialog In the same way as the Modify Nodes dialog different parts of the Modify Edges dialog will be activated depending on what files are present in the open graph archive Figure 9 shows the Modify Edges dialog after selecting an edge when only the topology file is present in the graph archive The Edge Properties section of the Modify Edges dialog is active but the Pathways Information section and describe changes in extended file button are not Basic edge information can be changed using the Edge Properties section As with nodes each edge has a unique ID assigned by FCModeler This unique ID is displayed in the Edge Properties section but can not be modified The certainty field is used to indicate the degree of certainty researchers have in the interaction represented by this edge The certainty can be either words or a number The edge type is set in the type field As with node types all edge types are listed in the edge t ype box Any of these types can be selected or a new edge type typed in the box The directed box indicates whether the edge is directed or 16 not only yes and no are the only allowed values Finally the strength field holds a text or numerical val
17. Microarray DATA The first row is the sample name list e g sample 1 sample 2 Data columns The first column is the locus name eg AT2G02010 the next data columns are the experimental values for each sample At present animation R can automatically detect and delete the extra spaces in the row and column names It can handle both format and 2 It can also automatically detect duplicated row names for microarray data one locus Id could appear several times in a single chip and output the duplicated list 4 Example Microarray data flat file format Format 1 At StarchSD1 Wt OL At StarchSD1 Wt 0L At StarchSDI Wt OL AT5G11160 6 64 6 41 7 12 AT2G02010 4 47 4 27 5 37 Format 2 Any Name At StarchSDI Wt OL At StarchSD1 Wt OL At StarchSDI Wt OL AT5G11160 6 64 6 41 TA AT2G02010 4 47 4 27 5 37 Here At StarchSD1 Wt OL is sample 1 and 6 64 is the value for this sample In this case AtStarchSD1 is the experiment name of replicatel WT is the genotype OL is the timepoint Format 1 is the default format of R produced data such as Bioconductor normalized data Format 2 is the default format of the data transferred from Excel file In this case the first element of first row can be any name our program just ignores this element 14 2 Other Data Other data like fold change data metabolomic data and proteomic data can be formatted in the same way Proteomic files currently can only be displayed according t
18. OSINE DEOKYINOSINE IDGD1 DGD2 DHS1 DHS2 DIACYLGLYCEROL Donor H2 ENR1 ERY THROSE 4P FERREDOXIN FRU umm v Figure 13 Identify Node dialog when a large graph with pathways and index information is loaded The nodes and edges of the graph have multiple properties associated with them Node properties include type e g gene RNA protein and location edge properties include type e g conversion regulation catalyst and strength Properties provide information about what the nodes and edges of the graph represent Each node and edge of the graph has a value for each property 7 1 Viewing Properties with the Property Viewer The Property Viewer Figure 14 shows the property values of all selected nodes and edges To open the Property Viewer select the Property Viewer menu item from the Interaction menu or right click on an item in the graph and select Detailed Properties from the pop up menu As nodes and edges are selected and deselected in the graph the Property Viewer window will update to show the information for the currently selected nodes and edges The Node Table and Edge Table frames on the left side of the Property Viewer display basic information for each selected node and edge Clicking on a row in either table will cause detailed information about that row s node or edge to appear in the right side window What information is displayed depends on how much data about the node or edge is available in
19. Written by Zach Cox Julie Dickerson Joset Etzel Pan Du Adam Tomjack FCModeler User s Manual December 2005 Copyright Julie Dickerson Iowa State University 2002 Table of Contents Introduction to BC Modelo us oe un end ee 5 2 EEModeler Installations user 5 2 1 Customizing the Gonti Surat ON gize ao sites za a a Fes dade 5 22 Ru nnnePCEModeler u a 5 2 SOC O IN DU gene ee e ee ee 6 3 1 APPO Gi 2 PATENI VOS pac E E E N 6 Je SD OS ec ee Nee 6 31 2 t polos VJ E 6 3 1 3 DIE Ke ROI tee ee ne ge need 6 3 1 4 So ree en ee iD eee ee ee 6 3 1 5 pathways x Mlese ee Sees 6 32 EINVAL TCS seee N A ER 7 32 MappIn ERO ee ee Tm 7 3 2 2 COOL IN ALES eu ndre aa 7 2 ANMAN eepe a 7 3 3 Reading and Writing Graphs in FCModeler anen eee rene enen eee ne eee eee enes eee 7 3 3 1 Readme a Zipped Graph Archive a d o Og em aie heces 7 329 2 Say me Gap MET N Eee oe unr are rT eT een 8 3 3 3 Saving an Imac Of th Graph as ae a at renim A 8 AY CODD LTD occ TUER 9 4 Simple Dot Ay OU bje nin e EMIL I Le E dE 9 42 Rk Cluster DON ay Out east aka 9 4 2 1 Layout XML PING 10 4 3 GENE DAVOS oco ce ceric Seatac tee Tbe iuc eas ane EIL OM ater eae ME IDE 11 4 3 1 ba E mer Me E S 11 4 3 2 AGE Mcr LL eescec eee o ae ahicseeactats 12 4 3 3 PAS pen 13 gt dnteractine VIN Graph N T VJ neo endura iu poe dep ee ta 13 5 1 Selectins NOGES an Edses nn ra RER 1
20. a particular characteristic such as their location or type the Node Properties tab is used in the same manner In more detail begin creating a new mapping rule by clicking either the Edge Properties or Node Properties tab depending on if the node or edge appearance should be changed The top If dropdown list box contains a list of all of the edge or node properties that are present in the current graph Select the property that you wish to base the rule on such as the edgeType When a property is selected in the first box the second dropdown list is automatically filled with all of the values for that property present in the graph Select the value that you want included in the rule such as Enzymatic reaction You may also create a compound rule involving two conditions such as If certainty is equal to indirect evidence or edgeType is equal to Catalysis then line color is red indicate the connector or or and from the list at the end of the first line and create the second rule from the second property and value boxes The mapping editor illustrated in Figure 17 is configured to make this compound rule The mapping rule illustrated in Figure 18 uses a color light blue which is not included in the list of basic colors Colors not shown in the dropdown list can be indicated by selecting other as the 23 color in the value list A standard color selection dialog vvill appear from vyhich any color can be chosen ee Node and
21. an not be undone 5 3 Edge Operations All operations that change edge information are performed using the Modify Edges dialog Figure 8 This dialog is opened by selecting Modi fy then Edges from the top FCModeler menu 15 Jo Modify Edges Pa edge e6 m Changes will be made to all graphs even if this is a subgraph Changes will be made to all graphs even if this is a subgraph Add New Edge Delete Selected Edges Add New Edge Delete Selected Edges Edge Properties Edge Properties Select the edge whose properties you want to Get Edge Select the edge whose properties you want to change in the graph then click this button change in the graph then click this button Edge Information Edge Information unique ID unique ID e6 certainty certainty 1 type type none v directed directed yes strenath strenath 1 head node head node w vv tail node tail node z z Pathways Information Pathways Information all pathways l inpathway s all pathways in pathway s Save Changes Close Figure 8 Modify Edges dialog Figure 9 Modify Edges dialog This dialog is used to add new after selecting an edge The graph edges delete edges and change the archive does not contain an index information associated with pathway or extended file so only existing edges It is opened by the Edge Information section selecting Modify then Edges is active from the top F
22. ane nnnn enen eee eee nene e vene eee eee nene eses 24 93 Other Subsrapn Creadon ODHODS anne 28 10 OS Ud EE 20 IOL reale an Animation P en s veton rae einen ua D od HL 20 10 1 1 Animation File Duration Factors aaa aaa naanaaaaaaaa eee eee nenen enen eneve zene eee enen ee vezeve nenen eses 29 10 1 2 Order Of Steps u the Animat ON cssc an ad dot a eiunnis 30 10 53 Savne the AMIMANON Pille sea so el 30 102 Vaewine am Animation File sessie NE etu ab Da 30 10 2 1 Opening an Animation Bile aaa nana eee e nenen eee eper eee eee 30 10 2 2 Using the Show Animation Dialog naaaaaaaaaaa aaa eee enen ene e ee eee eee eee ene ene vezen 31 11 Graph Iheoretie Operations Leni nije ae 31 DIE SUDSESDDS nee ie ee eier 32 11 2 Stronsiy Connected Components aa a are ao e mele bti tq St ae areas 32 11 5 Andie and Viewing Cycles aaa e 33 11 4 Bindings and VI VIN OP AT S itae Lee 34 11 5 Clustering Cycles WIE SOM tecto eed epe etu Eo ERE eaa bu tere ee a 34 12 Using R for Complex Visualization lessen enne nnne eene 33 r HE S DEALS ae ee TP 36 12 2 View Expression Data and Test the Con fi gUTatLON aaa aaa aaa eee e eee nenen eee 36 1223 USeOL ihe Animation Control Pane Lienee bitis Rt a 36 1 ant DI aE a 37 oz Data Pree proces stig stc IA in te ten Et uS 37 933 WOME DUE GINGER 37 1232 i Tolle Snes e 37 12 3 5 Data preprocessing details used in animation R aa ae eneve even eee ever 39 12
23. aph now Figure 25 P neighborhood of node AT3G58610 in Figure 26 Subgraph Creator dialog s edge type yellow The red node is the first neighbor the subgraph screen reaction node the second and the green nodes the third 9 5 Other Subgraph Creation Options The by identifying nodes directly or from a path cycle option provides an interface for several subgraph creation options All of these options let you specify the nodes that you want to include in the subgraph edges connecting these nodes will also be included If you know which nodes you want to include you can use the Identify Node dialog or FCModeler will read them from a text file plain text each line of the file a unique ID of a node 28 to include Alternatively a particular cycle or path can be selected using the path or cycle finder in the usual manner If a graph window is open you can create a subgraph containing nodes and edges that you selected in the graph using the by selection in the open graph option on the main screen Finally the subgraph can be restricted to edges of particular edge types Figure 26 by selecting the by edge type option This option should be used cautiously or the subgraph may consist of numerous unconnected nodes 10 Animation Animation files are used to display a series of mappings on an FCModeler graph creating a moving display An animation file is created using the Create Animation File dialog while it is displayed usin
24. archSD2 Wt 0L 0 WT At StarchSD2 Wt 0 5L 0 5 WT At StarchSD2 Wt 1L l WT At StarchSD2 Wt 4L 4 WT At StarchSD2 Wt 0D 8 WT At StarchSD2 Wt 0 5D 8 5 WT At StarchSD2 Wt 1D 9 WT At StarchSD2 Wt 4D 12 WT At StarchSD2 Wt 6D 14 WT At StarchSD2 Wt 8D 16 WT At StarchSD2 Wt 12D 20 WT At StarchSD1 ACLAI IL l ACLAI At StarchSDI ACLAI 0 5D 8 5 ACLAI At StarchSDI ACLAI 4D 12 ACLAI At StarchSD2 ACLAI IL 1 ACLAI At StarchSD2 ACLAI 0 5D 8 5 ACLAI At StarchSD2 ACLAI 4D 12 ACLAI 43 N NY N Fe e rt N N N N WV NV VY NY NY NN e e e e FF e e Re
25. archive Select one of the methods and click the Next button You may only choose one option at a time in the main Subgraph Creator screen but more than one subgraph creation method can be applied by going through the Subgraph Creator screen multiple times The screens for each of the individual subgraph creation methods e g Figure 23 have a set of three buttons in a frame at the bottom Create subgraph now Create subgraph then choose another method and Choose another method without making a subgraph now The Create subgraph now button creates the subgraph based on the previous selection and closes the Subgraph Creator while the other two buttons take you back to the main Subgraph Creator screen The Choose another method without making a subgraph now button cancels the current action while the Create subgraph then choose another method button creates the subgraph but instead of showing it holds it in memory and returns you to the main Subgraph Creator screen In this way a subgraph can be made by any combination of options For example you may have a large graph archive that has nodes from multiple pathways You may wish to view all of the nodes in a particular pathway that are within 5 steps of a particular node You can do this by first creating a subgraph by pathway name then clicking the Create subgraph then choose another method button then creating a subgraph by P neighborhood 9 3 Creating a Subgraph by Pathway Name Ifby pathway
26. ate node rules Add Mapping Rules Figure 19 Pathway tab of the Mapping Editor All Figure 20 Selection tab of the Mapping Editor edges in the Acetyl CoA Biotin network will be changed Mapping rules for eight nodes and six edges will be to have no connector end The node appearance will created the edges will be green and the nodes will be not be changed since create node rules was diamond shaped unchecked 8 4 Using the Mapping Editor Buttons After each mapping rule has been created click the Add Mapping Rule button on the tab The mapping rule will then be converted into FCModeler format and added into the list of mapping rules on the bottom portion of the mapping editor To view the effect of the current mapping rules click either the Apply or OK button at the bottom of the mapping editor The Apply button will apply the mapping rules to the graph in FCModeler without closing the mapping editor The OK button will apply the rules and close the mapping editor The Revert button at the bottom of the mapping editor deletes all mapping rules that may have been applied and returns the graph to its default appearance The Cancel button will close the mapping editor without applying any of the additional mapping rules that are present Any rules that were already applied will be unaltered however The list of mapping rules present in the mapping editor can be saved to an external file by clicking the Save Mapping File button The list
27. ation and resets it to the last frame The bottom slider labeled Delay controls the speed at which the animation is shown The length of time for which each step 1s shown on the screen decreases when the delay 1s set to 1 shortest or 2 and increases when the delay 1s set to 4 or 5 longest The relative duration of each step set by the duration factor remains constant even when the delay is altered 11 Graph Theoretic Operations Graphs are well studied mathematical objects and an entire area of mathematics called graph theory exists to study their properties A graph consists of two parts a set of objects called nodes or vertices and a set of relations between nodes called edges If a graph is undirected its edges are unordered pairs of vertices e u v v u while a directed graph called a digraph has ordered pairs for edges e u v v u The first node of a directed edge is called the tail and the second node is called the head A graph is typically denoted G V E where V is the node set or vertex set and E is the edge set FCModeler implements several graph theoretic algorithms that are useful for analyzing the properties of a specific graph These algorithms described below are also closely coupled with the graph view to visually present their results 31 11 1 Subgraphs For a digraph D V E a digraph H is a subdigraph of D if e V H cV D e E H c ED e E H v u e E D Iv u V H In other words
28. ation will be saved The list shows all values already inthe graph Select one of these or type in a new property unique ID 108412 Only change the molecule ID if necessary or a new node Use the property viewer to check molecule IDs of existing nodes molecule ID E151734 Index Information abbreviation s synonymis hist X histone X HP X Pathways Information all pathways in pathway s Jacety coA Biotin netv lt gt describe changes in extended file Save Changes Figure 6 Modify Nodes dialog after selecting a node The graph archive does not contain an index pathway or extended file so only the Node Information section is active Figure 7 Modify Nodes dialog after selecting a node The graph archive contains the index pathways and extended file so all sections of the dialog are active the node must be deleted before the node is deleted a node can not be deleted if it has edges To delete edges please refer to section 5 3 3 To delete an existing node open the Modify Nodes dialog Figure 5 and select the node s to delete in the graph Then click the Delete Selected Nodes button in the Modify Nodes dialog A message box will appear asking you to confirm that you wish to delete the selected node s If you click OK the node s will be permanently removed from the visible graph and the archive the node will no longer appear in any subgraph Deleting a node c
29. ber of in the right side box Change the pathway membership by selecting the desired pathway name and clicking the arrow keys After the desired node properties have been changed click the Save Changes button to save the changes Clicking the Cancel button will undo any changes that have been made since the node was selected 5 2 2 Adding New Nodes Open the Modify Nodes dialog Figure 5 Click the Add New Node button A unique ID will be generated automatically but you must specify the molecule ID name and type for the node Other node information such as its location abbreviations or pathway membership may be set if desired see section 5 2 1 for detailed instructions When all of the information has been entered click the Save Changes button The new node will be added to the upper left part of the graph After the Add New Node button 1s clicked the new node must be added you can not cancel the operation 14 d Modify Hodes Changes wil ke made fo all graphs even il lhc ie s tuli apti NB x l Pull Hew Minie Dekle Seksi Maes Selec Ge rede whee pr perters you ver bo change in the gregh Gren click Bes bulloni Bode een reme ME Ci e Dri Sh selected type amg Kocabon well b sve Te k t shows sl wies aed ni Graph Sect one ol merce or Gaqi in amp f e property unie Ky Boj id ID Guy shenje he molecule D i neceseary dr reer ride Lins he property viewer bo check molecule De of existing nodes i
30. bgraph Creator is shown in Figure 21 The all nodes and edges in memory option is selected so the new subgraph could contain any node and edge in the graph archive Ifthe graph in active graph window ONLY option is selected the new subgraph can only contain nodes and edges from the top open graph r X T E Subgraph Creator MAX E Subgraph Creator AX Select the subgraph creation method by pathway name Select graph to use to make the subgraph O by P neighborhood all nodes and edges in memory by identifying nodes directly or from a path cycle Next O by selection in the open graph O by edge type Next d Figure 21 Subgraph Creator dialog s first screen Figure 22 Main Subgraph Creator screen This The graph in active graph window ONLY screen lets you indicate how you want choose the option is disabled because no graph was open in nodes and edges in the subgraph Some of these FCModeler when the Subgraph Creator was options may be unavailable depending on the files started present in the graph archive 26 9 2 Choosing the Subgraph Creation Method The subgraph creation method is indicated on a frame of the Subgraph Creator dialog Figure 22 This screen lists the methods that are available some options may be unavailable depending on the files present in the graph archive For example you vvill not be able to create subgraphs based on pathway name unless a pathvvays file is included in the
31. cations so you can select an existing location or type in a new one 13 The molecule ID field can be modified if necessary FCModeler uses the molecule ID of each node to keep track of information about a molecule that may be shared among several nodes For example there may be one node in the graph to represent glucose n the cytosol and another node to represent glucose in the nucleus The location and unique ID of these two nodes will be different but the molecule IDs will be the same since they both represent glucose The molecule ID of any node can be viewed by right clicking the node and selecting Node Properties or by using the Identify Node dialog To change a node s molecule ID click the change button to the right of the molecule ID box onthe Modify Nodes dialog This will make the molecule ID box editable so that a new value can be entered The Modify Nodes dialog in Figure 7 shows the dialog s appearance when the graph archive contains pathways index and extended files All parts of the dialog are editable Abbreviations for the node are listed in the abbreviation s list and synonyms in the synonym s list For both lists new items can be added by clicking the add new button and existing items deleted by clicking the delete button after selecting the desired item The Pathways Information section lists all pathways in the archive that the node 1s not a member of in the left side box and all the pathways that the node is a mem
32. ciated metric and median Self organizing maps are used to find clusters of cycles obtained from a directed graph This approach is implemented using the JSOMap package for self organizing maps The map view window Figure 32 shows a grid of small graphs one for each unit of the map The map view window is opened by selecting Graph then Run SOM on Cycles after the Find Cycles dialog has been used to find all of the cycles in a graph Each window of the 34 map view dialog represents the model for that particular map unit The models are the generalized median of the set of cycles assigned to that map unit Figure 32 shows an example of a 4 by 4 SOM results in the map view window ve map view Jo de Graph Window Joe A A r Y a gt amp gt gt A LGLI T y g Y Prods v lt gt lt gt lt E k h y y ur t Y Y v E g s 2 ig lt 2 Ig gt A A INTI r a a y MI y l 7 77 4 Y v v wv nu Yv Figure 32 Map view window showing results of the SOM algorithm Each graph shows the model of the corresponding map unit which is the generalized median of the cycles assigned to that map unit 12 Using R for Complex Visualization Experimental profiling data can be visualized in FCModeler graphs using R Figure 33 shows the procedure of visualizing user data with FCModeler First import the data and process it by R a language and environment for statistical computing and graphics
33. cmodeler scripts directory Referring to this script may assist you in developing your own R animation scripts Another sample script is 39 network R which returns the graph structure and displays it as a subgraph the same as the original graph 12 4 1 Entry point The entry point of FCModeler to an R script is the function main FCModeler provides two parameters to R script FCMNodeList and FCMEdgeList which are the first two arguments of the function main Both FCMNodeList and FCMEdgeList are list class in R Their names are the node and edge attribute names For FCMNodeList it includes all the node attributes id molld nodeName nodeType location and etc For FCMEdgeList it includes all the edge attributes id head tail strength edgeType certainty etc A script may or may not use all these information in its production of mapping rules 12 4 2 Return Values Return values of main are in a list data structure At present it supports two types of returns One is the mapping rules which maps the graph in different colors and node shapes The other is the eraph structure which creates a subgraph in FCModeler The parameter type determines which type of return it 1s When type is mapping or without type information the return structure is of the form list type mapping mappingRules mappingRules exptName exptName timePoint timePoint duration duration refresh 0 where e mappingRules is a list in which th
34. created for each graph archive and the animation files are stored as separate files not part of the graph archives 10 2 Viewing an Animation File Animation files for a graph can be viewed after they are created The speed of the animation can be altered while it is being viewed and the animation can be paused at any time 10 2 1 Opening an Animation File The animation specified in an animation file is viewed using the Show Animation dialog as shown in Figure 28 To open the Show Animation dialog select Interaction then View Animation File from the top FCModeler menu A standard file open dialog will appear in which you should navigate to and select the animation file that you wish to view FCModeler will read the file and open the Show Animation dialog 30 Za Show Animation Close Figure 28 The Show Animation dialog used to display and control animations 10 2 2 Using the Show Animation Dialog The Show Animation dialog is used to control the display of animation files The top slider on the dialog labeled Frame indicates which step of the animation is currently being shown on the screen The slider always begins at step zero indicating that no mappings have yet been applied The play button B starts the animation while the pause button m pauses the animation at the current step The go to front button pauses the animation and resets it to the first zero frame while the go to end button Bi pauses the anim
35. de by creating xml files that match the given xml schemas A brief description of the type of information present in each xml file is now given for reference but no interaction with the individual xml files that make up each graph archive will be necessary unless new archives are made manually 3 1 1 contents xml The contents file contains background information about the data included in the zipped archive such as when and where it was created the organism that data refers to and the source of the data A list of Boolean values is used to indicate which of the optional files pathways index or extended are present in the archive 3 1 2 topology xml The topology file lists the nodes and edges of the graph The topology file contains the information required to draw the graph as well as very general information about each node or edge such as its strength subcellular location and default name 3 1 3 index xmi The index file lists all of the locations names abbreviations and synonyms for each moleculeID included in the topology file 3 1 4 extended xml The extended file contains detailed reference information such as the journal article in which a particular connection vvas described or the person that entered a node for every node and edge in the topology file 3 1 5 pathways xml The pathways file lists all of the nodes and edges involved in a particular pathway as well as each pathway s name and ID 3 2 Individ
36. deler topology file The id from and to fields are required 13 References 13 1 Publications relating to FCModeler Cox Z February 28 2002 JsOMap a Java based Self Organizing Map package http jsomap sourceforge net Date accessed June 18 2002 Dickerson J A D Berleant et al to be published in 2002 Creating and Modeling Metabolic and Regulatory Networks Using Text Mining and Fuzzy Expert Systems Computational Biology and Genome Informatics C H Wu P Wang and J T L Wang World Scientific Dickerson J A D Berleant et al 2001 Creating Metabolic Network Models using Text Mining and Expert Knowledge Atlantic Symposium on Molecular Biology and Genome Information Systems and Technology CBGIST 2001 Durham North Carolina Dickerson J A Z Cox et al 2001 Creating Metabolic and Regulatory Network Models using Fuzzy Cognitive Maps North American Fuzzy Information Processing Conference NAFIPS Vancouver B C 13 2 Open Source Code Used in FCModeler Dot graph layout routine from the Graphviz package of AT amp T http www research att comsw tools graphviz Diva framework graph nodes and edges http www gigascale org diva Java SDK http java sun com Tulip GEM Routine for graph layout http www tulip software org 14 Appendix R Script File Formats The data file is a tab delimited text file Excel files can be easily saved as tab delimited text files 14 1
37. e Layout Algorithm for Undirected Graphs by Frick Ludwig and Mehldau This code is a Java translation of the Frick s 11 implementation in C code GEM turns every node into an electron and every edge into a stretched spring and places a gravitational force at the barycenter of the layout A node is attracted to all nodes adjacent to it and is repelled by every node whether or not it is connected by an edge In addition there is an attract ve gravitational force between each node and the barycenter of the graph GEM has three main loops the insertion loop the arrangement loop and the optimization loop The insertion loop is where the nodes are initially placed The closer a placement is to the final layout the faster the arrangement loop runs The arrangement loop does most of the work getting the nodes to their final positions Following the example of Tulip we did not implement the optimization loop Jo FCModeler Jag File View Layout Graph Interaction Modify Tools Window ad AR Rose el Figure 4 Example of aGEM layout using the same graph as in Figure 2 and Figure 3 4 3 2 AGEM This is the new spring embedder algorithm that differs significantly from GEM It uses much of the framework of the GEM algorithm but the heart of it is different AGEM removes the repulsive force between pairs of nodes reverses the direction of the gravitational force to make it repulsive and retains the attract ve spring forces between
38. e mapping rules are stored This field is mandatory e duration is the time difference between two sets of mapping rules If the difference is negative or the time information is not available just use unit duration By default it is 1 e refresh is used to tell FCModeler whether to refresh the graph display before applying the new mapping rules By default it is 0 this means it will add the new mapping rules on the old graph e exptName is a list of Affymetrix experiment names at each time point or experiment By default it uses a format like experiment 1 e timePoint is the time point of each experiment If not provided it uses the experiment index number When type is graph the return structure is of the form list type graph nodeAttName nodeAttName edgeAttName edgeAttName nodeInfo nodeInfo edgeInfo edgeInfo e nodeAttName lists the node attribute names included in nodelnfo matrix e edgeAttName lists the edge attribute names included in edgeInfo matrix e nodelnfo is a matrix Each row represents one node each column represents one particular node attribute such as id nodeName or location These are the same attributes as the FCModeler topology file The id field 1s required 40 e edgelnfo is a matrix Each row represents one edge each column represents one particular 99 66 edge attribute such as id from to or edgeType These are the same attributes as the FCMo
39. er gt lt cluster gt lt layout gt The lt rank gt tag is used to specify the nodes that should be placed in a certain horizontal rank Each rank has a label specified by the label attribute which is shown on the left hand side of the graph view Nodes are selected using the same type of XML as in the property to visual attribute mappings see section 7 Similarly the lt c uster gt tag 1s used to specify nodes to place in a cluster Each cluster is surrounded by a rectangle and has a label specified by the 1abe1 attribute which is shown on the upper left of the cluster The lt cluster gt tag uses the same node selection mechanism as the lt rank gt tag lt cluster gt tags can be nested inside each other creating nested clusters as shown in clusters EandF and OnlyG above 4 3 GEM Layouts The GEM family of layouts are also available in FCModeler These are GEM AGEM and FastGEM and are derived from code developed by the Tulip project www tulip org GEM is the standard layout in the GEM family It can handle disconnected graphs but takes the longest to run the quality is good and consistent AGEM runs much faster than GEM but does not handle disconnected graphs well and the quality is only fair and much more inconsistent FastGEM uses AGEM to do the initial layout then GEM to refine the layout making quality layouts more consistently than AGEM 4 3 1 GEM This is the standard layout as detailed in A Fast Adaptiv
40. g the View Animation File dialog 10 1 Creating an Animation File Before an animation can be viewed an animation file describing the animation must be created These files are made using the Create Animation File dialog shown in Figure 27 To open the Create Animation File dialog select Interaction then Create New Animation File from the top FCModeler menu Each animation file consists of a series of steps each of which is made of mapping rules The Add New Step to Animation button onthe Create Animation File dialog brings up the Mapping Editor which is used in the regular manner see 8 The Mapping Editor to construct the mapping corresponding to that step 2 Create Animation File Oleg Create an animation file by making a set of mappings one for each step af the desired animation The animation will cycle through the mappings in the order shown here starting at the top Add New Step to Animation Duration factor for new step 1 Update Delete selected step Save Animation File Figure 27 TheCreate Animation File dialog as appears when it first opens 10 1 1 Animation File Duration Factors Each step in an animation file has a duration factor associated with it in addition to the mapping rules The duration factor is used to indicate the relative length of time that the mapping for that step should be displayed The default value for the duration factor is 1 so setting a step s duration factor to 4 causes it to be displa
41. http www r project org Then perform data processing which includes preprocessing color mapping and producing mapping rules for FCModeler The communication between R and FCModeler is via an XML based protocol Simple Object Access Protocol SOAP http www w3 org TR soap Finally visualize the experimental data in FCModeler by creating mapping rules to change the colors of particular nodes and edges Experimental Data Processing Java to R FCModeler Data in R linker SOAP Visualization Figure 33 Visualizing user data with FCModeler 35 12 1 R Configuration R is freely available at http www r project org download and install the most recent version for your system if you do not already have a copy Two R packages must also be installed tkrplot and XML These packages are also freely available for download either from CRAN v a the R website or from within R itself select Packages then Install Packages from the top menu To configure R to work w th FCModeler system environment variables must be set e In Windows set the R HOME environment variable Click Start then Control Panel In the Control Panel click the System icon then the Advanced tab On the Advanced tab click the Environment Variables button In the dialog click the New button in the System Variables frame then create a new environment variable pointing to the R installation location e g Variable name R HOME and Variable Value C Program Files R rw2
42. ift key to select blocks of entries Depending on the graph selecting one row in the Identify Node list may identify more than one node in the graph Many nodes may share the same synonym name or molecule ID 19 A Identify Node ced Pe Identify Node aax Properties select all unselect all show items molecule IDs _node names node types Type to scroll the list Locations select all show items none Pathways select all show items Cancel Figure 12 The Identify Node dialog This dialog is used to identify nodes by name type location pathway or other properties 7 Node and Edge Properties Properties select all unselect all show items C molecule IDs node names node types synonym mi E Locations show items cytosol E mitochondria plastid 1 plastid inner membrane M D ga gt a e select a show tems c 1 Jglycosylolyceride biasy JEEE 1 Update View plastid outer membrane v chorismate biosyrthesi fatty acid elongation s glucose 1 phosphate m isoleucine biosynthesis wi decani da risas Mu asc E Type to scroll the list CO A CPD 1301 CPD 1302 CPD 172 CPD 451 C526 1 icyatathionine gamma synthase ICYS cysteine synthase IDEHYDROQUINATE DEOXY RIBOSE 1P DEOX Y ADENOSINE DEOKYGUAN
43. ill be red but if the second is applied before the first these lines will be blue 23 The order in which the mapping rules are applied can be changed by clicking the arrow buttons to the left of the list of mapping rules The up arrovv E vvill move the highlighted rule higher in the list while the down arrow il will move the highlighted rule lower in the list A mapping rule can be constructed and added to the list of mapping rules by typing it in the box to the left of the Manual Entry button and clicking the button Complex rules can be created in this manner but the rules must be formatted 1n the same way as those created using the dropdown lists 9 Subgraph Creation The Subgraph Creator is used to make a new graph from a bigger graph For example you may have a graph archive that has thousands of nodes and edges This graph 1s too big to display at once Instead you use the Subgraph Creator to tell FCModeler which part of the graph you want to see such as all nodes and edges within 4 steps of a particular node FCModeler will make this new graph a subgraph of the graph archive and open a new window to show it 9 1 Starting the Subgraph Creator dialog Open the Subgraph Creator dialog by selecting Graph then Create Subgraph from La the top FCModeler menu or by clicking the toolbar button The Subgraph Creator may also be started when a graph is opened if the graph is too big to display automatically The first screen of the Su
44. l find all cycles in the graph or you can restrict 1t to searching for cycles of a particular length or containing particular nodes To restrict the cycles to particular nodes click either the Identify nodeor Select node buttons The Max cycle length box is used to set the maximum cycle size in number of edges Click the Find cycles button to find cycles of the length and containing the nodes you specified or click the Find A11 Cycles button to find all cycles in the graph 33 11 4 Finding and Viewing Paths A path is the collection of nodes and edges that lead from one node to another node The Find Paths dialog Figure 31 in FCModeler searches for all paths of the specified length between two nodes Open the Find Paths dialog by clicking the toolbar button or selecting Graph then Find Paths from the top menu Set the starting and ending node for the path using either the Identify Node dialog by clicking the appropriate Identify Node button or by selecting the nodes directly in the graph select the node then click the appropriate Select Node button The max mum path length is set to unlimited by default change this to the maximum path length you want each edge is counted as one unit of length and click the Find Paths button to perform the search All paths found will be put in the list box click on the path name to view itin the graph Fie Wew Layout Graph Inberachon Med y Tosk Window Fm wew Layout Graph intersection Mody io Wi
45. le nodes and or edges J click and drag around multiple node and or edges 5 2 Node Operations All operations that change node information are performed using the Modify Nodes dialog Figure 5 This dialog is opened by selecting Modify then Nodes from the top FCModeler menu 5 2 1 Modifying Node Information Open the Modify Nodes dialog Figure 5 Only one node s information can be changed at a time Select the node whose information you want to modify in the graph then click the Get Node button on the Modify Nodes dialog FCModeler will read all the available information about the node and display it on the Modify Nodes dialog Different parts of the dialog will be active depending on the types of files that are present in the open graph archive Only information for files that are present can be changed The Node Properties section of the Modify Nodes dialog will always be active since this information is present for every node in every FCModeler graph see Figure 6 The unique ID is set by FCModeler and can not be modified but all the other properties can be changed The name box is the name that will be used to label the node on the graph The t ype box is the node s type All the node types in the graph are listed in the drop down box You can select one of the existing node types for this node s type or make a new one by typing in the t ype box and pressing the return key Similarly the Location box lists all the existing node lo
46. lusters for the rank cluster layout are specified n a layout XML file The XML file used in the layout for Figure 3 is shown below lt xml version 1 0 standalone yes gt lt DOCTYPE layout lt ELEMENT layout rank cluster gt lt ELEMENT rank atom composite gt lt ATTLIST rank label CDATA REQUIRED gt lt ELEMENT cluster atom composite cluster gt lt ATTLIST cluster label CDATA REQUIRED gt lt ELEMENT atom EMPTY gt lt ATTLIST atom property CDATA REQUIRED value CDATA REQUIRED gt lt ELEMENT composite atom composite connective atom composite gt lt ELEMENT connective EMPTY gt lt ATTLIST connective type and or REQUIRED gt gt lt layout gt 10 rank label 2 rankl atom property type value typel gt lt rank gt lt rank label rank2 gt lt atom property type value type2 gt lt rank gt lt rank label rank3 gt lt atom property type value type3 gt lt rank gt lt cluster label AandB gt lt composite gt lt atom property label value a gt lt connective type or gt lt atom property label value b gt lt composite gt lt cluster gt cluster label EandF gt lt composite gt lt atom property label value e gt lt connective type or gt atom property label value f gt lt composite gt lt cluster label OnlyG gt lt atom property label value g gt lt clust
47. n the subgraph Indicate Nodes The subgraph will be based on the nodes in this box Use the buttons to add and remove nodes PYRUVATE Select the pathways to include in the subgraph chorismate biosynthesis Aracyc fatty acid elongation saturated Aracyc glucose 1 phosphate metabolism Aracyc glycosylglyceride biosynthesis amp racyc isoleucine biosynthesis amp racyc nucleotide metabolism amp racyc Remove ribitol utilization amp racyc Identify Nodes Named Pathway Current Selection in Graph Read from File P 2 Create subgraph then choose another method Create subgraph now Choose another method without making a subgraph now pe Create subgraph then apply another method Create subgraph now Choose another method without making a subgraph now Cancel Figure 23 Subgraph Creator dialog s pathway Figure 24 Subgraph Creator dialog s p subgraph screen The screen is set up to create a neighborhood subgraph screen The screen is set up subgraph of all nodes in the glucose I phosphate to create a subgraph of all nodes within two steps of metabolism pathway the pyruvate node A FC Modeler e eee a9 BO PR 2222225555555 5 35t SA EJ Subgraph Creator Joe Only edges of the selected types will be shown in the graph Catalysis Enzymatic reaction Translation Create subgraph then choose another method Create subgraph now Choose another method without making a subgr
48. names of the selected type By default it will show all the RNA names in which you can select part or all of them and view their profiles By clicking a profile it will be highlighted and the name of corresponding entity will be shown in the status bar and highlighted in the list box as shown in Figure 35 You may also highlight the profiles by double clicking the name in the list box The profiles can be standardized or in usual scale od Animation Control Panel File Data Type Data Analysis View Data Help Input Data Select Data File data sample microarray Select File View Data Select Experiment Info File data sample_exptlnfo te Select File Data Preprocess Setting View Info Select Subset of Data Fold Change between GenoT ype Average Heplicates Scale of Expression Value Log Unlog Standardize Each Profile Output Setting Use Equal Time Interval w Set Animation Colors Change Colors Save Animation File E OF welcome to Animation Control Panell Data Selection Panel Select Genotype ACLAT Ww wT Ww Select Replicate 1 m 2 iw Select TimePoint Oh u5iw iw 4w w x Figure 34 Animation Control Panel dialogs ae w 9 iw jes Animation Control Panel Fie Data Type Data Analysis Help Input Data Select Data File D femodeler femodeler Select File View Data Select Experiment Info File Select File Data Preprocess Setting
49. ndies Finami abbreviations minns n Patines Informalion LT ini patres Gere Figure 5 Modify Nodes dialog This dialog is used to add new nodes delete nodes and change the information associated with existing nodes It is opened by selecting Modify then Nodes from the top FCModeler menu 5 2 3 Deleting Existing Nodes The Modify Nodes dialog is also used to delete nodes from the graph All edges attached to Jo Modify Nodes m 2b Modify Nodes m Changes will be made to all graphs even if this is a subgraph Node Properties Select the node whose properties you want to change in the graph then click this button Node Information name aj type none v location none vi Only the selected type and location will be saved The list shows all values already in the graph Select one of these or type in a new property unique ID a Only change the molecule ID if necessary or a new node Use the property viewer to check molecule IDs of existing nodes molecule ID 0 Index Information abbreviation s synonymis Pathways Information all pathways inpathway s Save Changes Changes will be made to all graphs even if this is a subgraph Node Properties Select the node whose properties you want to change in the graph then click this button Node Information name Histone protein X type protein complex v location nucleus i Only the selected type and loc
50. ndow Q amp a 8 8 O a O m so e amp kH O t 42 PeCiAcheyenne vec lipse cmo deleribin graphs yclnTest zip OO Find Cycles BE Fie Piter S Find Paths Bez Fiter Fid yet barinj Lian d Ein Kodi hun to nii n noe Trom Eee gram view Add iode or Ihe k ndit Node buttons To k n a roge by name or properties PEATE Sie ge S TE l ketiy rana Simi node Shar Mode usi Vientihy Node sent ode AL 15 Raroa node End None T i Pal Lereahe ame Find Pat r Palle Four Firmen arimbi nd Mery cyein berlin Uin miani Find cyrisa Find 4 Cycles s gt 4 gt Figure 30 TheFind Cycles dialog Three cycles Figure 31 Find Paths dialog The dialog found all containing the node u blue were found The paths from node u to node z in pink One path was selected cycle u 1 a b v is highlighted in the graph found and highlighted 11 5 Clustering Cycles with SOM Cycles obtained from directed graphs may be s milar to each other based on their node and edge content Thus clustering algorithms may be used to find natural groups of similar cycles Prior to clustering a distance metric and generalized set median must be defined for the objects to be clustered Several possible representations for the cycles are discussed including strings graphs and vveighted sets Weighted sets are chosen because of the simplicity of the asso
51. node after which FCModeler will select it in the graph and move the display so that the node is in the center The dialog is opened by selecting View then Find Node from the top FCModeler menu If you know the exact name of the node it can be found by typing its name in the Name of node to locate box onthe Find Node dialog and clicking the Find button Alternatively one or more nodes can be identified using the Identify Node dialog Open the dialog by clicking the Identify Nodes button then identify the node s you wish to find in the normal way see section 6 Using the Identify Node Dialog for more information Click OK in the Identify Node dialog to close it then Find on the Find Node dialog BB Find Node Joe Name of node to locate Identify Nodes Close 18 Figure 11 The Find Node dialog This dialog is used to locate one or more nodes in the visible graph 6 Using the Identify Node Dialog The Identify Node dialog Figure 12 and Figure 13 1s used throughout FCModeler to identify nodes It does not alter the graph or graph view in any way but rather lets you indicate which nodes you are interested in even if the nodes are not present on the screen For example you may w sh to make a subgraph of a graph that s too large to view The Identify Node dialog lets you select the nodes that you want to include in the subgraph The Identify Node dialog consists of two halves The right side contains a list while the left
52. node include a reference link which opens the default web browser when clicked 8 The Mapping Editor The Mapping Editor Figure 16 is used to change the appearance of a graph either of individual nodes and edges or of all nodes and edges in a particular category For example all nodes in the graph of type gene can be displayed with an elliptical node shape or one edge can be displayed in red To open the Mapping Editor either select the Mapping Editor menu item from the View menu or click the toolbar button Mapping rules are statements that describe the appearance changes to be made to the graph such as If edgeType is equal to enzyme then connector end is circle If nodeType is equal to polypeptide and location is equal to unknown then node outline color is red or If id is equal to A154d then node fill color is blue These rules are created using the dropdown lists on the Edge Properties Node Properties Pathway and Selection tabs of the Mapping Editor The Mapping Editor allows the following attributes to be changed e nodes node fill color node outline color node shape e edges connector end line color line thickness line type 22 d Fcio delei Jogi File View Layout Graph Interaction Modify Tools Window anti Mappings Jejm jleiBlolel 2 rae cii C Documents and Settings jaetzel CRCD 1 DesktopimodifyTest1 zip rats ITIGI UN acinyd Co Herc If edgeType v is equal to
53. o locus ID Work on visualization of protein modifications and protein complexes is in progress Metabolomic data 1s displayed regardless of subcellular compartment Compartmentalization function is being developed 14 3 Experiment information file format an example This s a tab separated text file that describes an experiment in which two genotypes ACL and WT were grown under short day conditions and sampled at 11 time points WT or 3 time points ACL during a diurnal cycle Two replicates were made Each experiment group is composed of the UNIQUE ID and its attributes UNIQUE ID includes the experiment name and sample name It MUST be identical to the sample name on the microarray data file TIMEPOINT is the time point of each sample GENOTYPE They are WT var Columbia and ACLAI antisense ACLAI Fatland Nikolau Wurtele 2004 in this example TREATMENT in this case there is no treatment so column is left blank REPLICATE Two replicates are available in this case AUTHORS Carol Foster Li Ling Martha James Alan Myers Basil J Nikolau Eve Syrkin Wurtele c ck KE cb Gb HHH Gk UNIQUE ID TIMEPOINT GENOTYPE TREATMENT REPLICATE At StarchSD1 Wt OL 0 WT 1 42 At StarchSD1 Wt 0 5L 0 5 WT At StarchSD1 Wt 1L l WT At StarchSD1 Wt 4L 4 WT At StarchSD1 Wt 0D 8 WT At StarchSD1 Wt 0 5D 8 5 WT At StarchSD1 Wt 1D 9 WT At StarchSD1 Wt 4D 12 WT At StarchSD1 Wt 6D 14 WT At StarchSD1 Wt 8D 16 WT At StarchSD1 Wt 12D 20 WT At St
54. o the current graph by selecting Apply Coordinate File from the Layout menu then indicating the file that is to be used Coordinate files must have been previously created by FCModeler on that graph 3 2 3 Animation Multiple sets of mapping rules can be combined into an animation file The animation can then be viewed using the Show Animation dialog Animation files are plain text files with additional XML style lines added 3 3 Reading and Writing Graphs in FCModeler 3 3 1 Reading a Zipped Graph Archive To open a graph archive in FCModeler either select the Open Graph menu item from the File menu or click the amp button on the toolbar A standard file selection dialog will appear from which the graph archive to open can be chosen If the pathToGraphs line was filled in the FCModelerConfig txt file as described in section 2 1 the file selection dialog will open in the indicated directory FCModeler graph archives will generally end in zip to indicate that they are zipped archives but may end in any extension 3 3 2 Saving a Graph XML File To save the current graph as a zipped archive either select the Save Graph menu item from the File menu or click the toolbar button The dialog shown in Figure 1 will appear The radio buttons in the Nodes and Edges to Save andOther Information to Save frames let you tell FCModeler what you want to save If you have made subgraphs you can save either the information in the top subgraph only the
55. on of Java 1 4 or higher which can be downloaded free of charge from http java sun com 2 1 Customizing the Configuration Before FCModeler can be run the configuration file fcmodelerconfig txt must be modified The fcmodelerconfig txt file will be installed in the directory in which the FCModeler distribution was unzipped Locate this file and open it in a text editor such as notepad The first line of fcmodelerconfig txt should be modified to indicate the entire path to the dot exe file that was included in the FCModeler distribution For example if the distribution was unzipped in C Program Files FCModeler then the pathToDot line of femodelerconfig txt should be modified to read pathToDot C ProgramFiles fcmodeler dot exe The pathToGraphs line can be modified or left blank If you would like FCModeler to start in a specific directory when opening or saving files enter this directory in the pathToGraphs line If this line s left blank FCModeler will start in the default user directory for the computer when opening or saving files For example if you will store most FCModeler files in the graphs directory that was created when FCModeler was unzipped then the pathToGraphs should be modified to read pathToGraphs C ProgramFiles fcmodeler graphs After the change to pathToDot and pathToGraphs if desired are made save fcmodelerconfig txt as a plain text file 2 2 Running FCModeler FCModeler is started by double clicking on
56. orithm for finding the SCC s of a digraph D is extremely simple and is based on two modifications of depth first search DFS 1 Compute an acyclic ordering of the nodes using DFS 2 Compute the converse D of D 3 Perform DFS on D using the ordering from Step 1 Each DFS tree is a SCC of D To find the strongly connected components of a graph in FCModeler select the Find Strongly Connected Components menu item from the Graph menu After performing the above algorithm FCModeler lists the SCC s Figure 29 Clicking on an SCC in the list selects its nodes and edges the graph A File View Layout Graph Interaction Modify Tools Window aa ala eialo l e Anew subgraph Jes amp Strongly Connected Components Joe reaction DI amp CYLGL Y CEROL reaction CPD 451 reaction H20 v lt gt Figure 29 Example of selecting strongly connected components 11 3 Finding and Viewing Cycles A path in a digraph is an alternating sequence of nodes and edges vjejvze2v3 Vk 1 k 1Vk such that tail e v head e v and all nodes are distinct A path can be viewed as starting at node v and following edges through the graph until node v is reached If v v the path 1s called a cycle The Find Cycles dialog Figure 30 is used to find cycles in FCModeler The dialog is opened by clicking the toolbar button or selecting Graph then Find Cycles from the top menu The dialog wil
57. ssion Value can be set to either Log default or Unlog For microarray data the program will automatically determine the data s original scale by checking the data s maximum amplitude if minimum amplitude is less than 0 the data is in Log scale then transfer the data to the scale the user specified The option to Standardize Each Profile to0 mean and 1 variance is provided This is useful for finding correlational patterns Without standardizing we cannot see the similar changing patterns among nodes because their amplitudes are not comparable with each other 12 3 3 Output Setting frame Ifthe Use Equal Time Interval box is checked the time interval between animation frames will be equal otherwise real time intervals computed based on the sample time will be used The Set Animation Colors button opens a dialog to change the default animation colors As shown in Figure 34 the default animation is based on the three color mapping the high value color red the middle value color yellow and the low value color blue Check the Save Animation File option to output an animation file for future use The saved animation file can be loaded into FCModeler later using the Show Animation File dialog see section 10 2 2 Using the Show Animation Dialog 12 3 4 View Data Profiles The user can view the data profiles by clicking the View Expression Profiles option under the View Data menu item as shown in Figure 35 A GUI will show all the entity
58. t evia 544 17648 Node 471616350 is currently selected Address Please type any url to surf Leo rk Topology Information Node name AT1G16350 Node type polypeptide location cytosol Molecular id E8312 Node id 8312 kk Index Information synonym AT1G16350 synonym AT1G16350 MONOMER synonym INOSINE 5 MONOPHOSPHATE DEHYDROGENASE were Pathway Information in pathway nucleotide metabolism Aracyc Backeround Information Data source MetNet database Figure 14 Property Viewer showing property values of selected nodes and edges The right side shows detailed information for the node whose row is selected in the Node Table AT1G16350 7 2 Viewing Properties of a Single Item You can also view the property information for any particular node or edge without using the Property Viewer Right click the node or edge and select Node Properties or Edge Properties if an edge from the pop up menu A window will appear as shown in Figure 15 This window shows the same information as the right side panel of the Property Viewer 21 A e File View Layout Graph Interaction Modify Tools Window File Edit View Go Bookmarks Tools Help 5 m amp amp 0 e m E v EJ e 5 http www arabidopsis org servlets TairObject type locus amp name AT4G36530 AC Documents and Settings jae
59. the File menu and indicate the file and format desired 4 Graph Layout To v ew a graph a graph layout algorithm must compute positions of the node and edge figures Many different graph layout algorithms exist FCModeler currently uses Dot and GEM to compute its layouts 4 1 Simple Dot Layout There are two types of layout that can be computed by Dot The first is a generic layout called the Simple Dot Layout When a graph is opened in FCModeler Simple Dot Layout is applied by default It can be applied at any time by selecting Dot Layout from the Layout menu Figure 2 shows a graph layout done using the simple dot layout La FCModeler Jog File View Layout Graph Interaction Modify Tools Window ea aaleialoiel JE AC cheyenne eclipse femodeler bin graphs cycleTest zip JIZJES Figure 2 Example of the simple dot layout using a small graph 4 2 Rank Cluster Dot Layout Dot can also be used to compute a more customized layout Based on their values of certain node properties the node figures can be placed on horizontal ranks or into clusters When a graph is open in FCModeler select the Dot Rank Cluster Layout menu item from the Layout menu An open file dialog box is shown in which a layout XML file must be selected see below Figure 3 below shows the same graph as in Figure 2 using the rank cluster layout tE ae ja Figure 3 Rank cluster dot layout 4 2 1 Layout XML File The ranks and c
60. the file run bat which is created in the root FCModeler directory when the distribution was unzipped If desired a shortcut to this file can be created in Windows by right clicking on run bat and selecting Create Shortcut from the pop up menu This shortcut can be moved to the desktop or any other convenient location 3 Sources of Input FCModeler reads and writes graphs in its own XML format Each graph consists of two or more XML files which are zipped into a single archive Other XML files such as mapping files are read by FCModeler after a graph has been loaded These files are used to save information about the colors and line styles that should be used to draw the graph Each zipped graph archive may have multiple mapping files associated with it 3 1 Zipped Graph Archives The zipped graph archives used by FCModeler are made up of two or more XML files each of which are in a different format and hold a different type of information A zipped archive may only have one copy of each type of file Every graph archive must include a contents and a topology file The graph archive may also include an index extended and pathways file if the relevant information is available Each xml file has a schema defining its format Several example data archives are included in the graphs directory of the FCModeler distribution and data archives can be downloaded from the METNET database or FCModeler web sites Alternatively new archives can be ma
61. tzel CRCD 1Wesktop modifyTest1 zip LI etc L work KI temp Salon com Daou R vt a ir Home About TAIR Sitemap Contact He Search Tools Arabidopsis Info News Links FTP Stocks Gene AO nn 1 lt 7 Properties for node AT4G36530 BAX Locus AT4G36530 T i y i gt Date last modified 2003 05 02 j Address l airObject type Iocus amp name AT4G35530 TAIR Accession Locus 2115440 Representative Topology Information Other names AP22 96 AP22 96 DS Node name AT4G36530 pra Gene Models Name Description Source Node type RNA ATAG36530 2 hydrolase alpha beta fold family protein AGI TIGF Node location cytosol splice variant low similarity to hydrolase ee Sphingomonas sp G1 3426124 Molecular id E91637 contains Pfam profile PF00561 Node id 91639 hydrolase alpharbeta fold family tik Extended Information Tair Link for AT4G36530 Annotations Category Relationship Type Keyword 2 GO Biological Process involved in aromatic compoul Description testing Lots of modified amp created GO Cellular Component located in chloroplast entries GO Molecular Function has catalytic activity hy none hydrolase activity Sa on O 0 0 Annotation Detail atabase name tair RNA Data z p www arabidopsis ordg servlets TairObject type locus amp na One channel ara element HL Sigel avo signal Arravs nama 2 intanciti liota nrrari narenntiln etd Figure 15 Dialog showing the properties for a single node The properties for this
62. ual Files The mapping coordinate and animation files can be read by FCModeler but are not included in a zipped archive Multiple mapping animation and coordinate files can be used with each zipped archive as these files specify how to display the graph and multiple display parameters can be used with each graph 3 2 1 Mappings Node and edge properties can be mapped to the visual attributes of node and edge figures For instance all of the nodes in the nucleus can be drawn in pink while all of the nodes in the mitochondria in green These mapping rules which are constructed using FCModeler s Mapping Editor can be saved in mapping files As many mapping files as desired can be created and used with each graph Mappings are described in detail in section 7 of this document 3 2 2 Coordinates The coordinates of node and edge figures calculated by the graph layout algor thms can also be saved in XML format These XML files contain all of the information necessary to restore the layout to a specific form at any time which may save time f a very large layout needs to be calculated As w th mapping files as many coordinate files can be used with each graph archive as desired 3 2 2 1 Creating Coordinate Files A coordinate file can be created by selecting the Save Coordinate File from the Layout menu in FCModeler A file will be written in the indicated location 3 2 2 2 Reading Coordinate Files A coordinate file is read and applied t
63. ue indicating the strength of the reaction represented by the selected edge The head and tail node of the selected edge can also be changed using the Edge Information section of the Modify Edges dialog The head node is the node that the edge points to the tail node is the node the edge comes from To change the head or tail click the node in the graph that you want to be the new head or tail then click the corresponding select node button on the dialog The dialog w ll show the new node s name in the head node ortail node box but the graph vvill not be updated until the changes are saved If a pathways file is present the Pathways Information section of the Modify Edges dialog will be active This section works in the same way as the Pathways Information section of the Modify Nodes dialog see 5 2 1 Modifying Node Information 5 3 2 Adding New Edges To add a new edge to the graph click the Add New Edge button in the Modify Edges dialog FCModeler will automatically create a new unique ID for the edge but you need to set the certainty strength type and directed fields You must also select the nodes to use as the head and tail for the new edge After setting the properties for the new edge click the Save Changes button and the new edge will appear in the graph 5 3 3 Deleting Existing Edges To delete an existing node open the Modify Edges dialog Figure 8 and select the edge s to delete in the graph Then click the Delete Selected
64. yed four times as long as the default while setting the duration factor to 0 5 causes it to be displayed half as long as the default 29 The duration factor for a step can be set when the step is added by typing itin the Duration factor for nev step box before the Add Nev Step to Animation button is clicked or by selecting the step in the list of steps on the Create Animation File dialog typing the new duration in the Duration factor for new step box and clicking the Update button 10 1 2 Order of Steps in the Animation The steps in the animation file vvill be shovyn in the order in vyhich they appear on the Create Animation File list Each new step is added to the bottom of the list so the steps will be displayed in the order in which they were created unless the order is altered To alter the order in which the steps will be shown select the step to move then click the up or down arrow A step can be deleted by clicking the Delete Selected Step button after the step has been selected 10 1 3 Saving the Animation File After all of the steps have been added to the animation file and are shown on the Create Animation File dialog in the correct order the animation file can be saved by clicking the Save Animation File button This button will cause a standard save dialog box to be displayed in which the desired location and name for the animation file can be specified As with mapping files as many animation files as desired can be
65. you only want to change the node or edge attr butes deselect the corresponding check box Finally click the Add Mapping Rules button which will create mapping rules describing the appearance of each selected node and edge 8 3 Using the Pathway tab If the graph archive contains a pathway file the Pat hway tab Figure 19 can be used to change the appearance of all nodes and or edges in a particular pathway All pathways present in the graph archive are listed in the pathways box by default select the list pathways in window only option to restrict the list to those pathways that have at least one member in the visible graph As with the Selection tab mapping rules can be made for the nodes or edges by checking the appropriate boxes max Node and Line Mappings Node Properties Edge Properties Pathway Selection list all pathways list pathways in window only Acetyl CoA Biotin network Expert User pathways edge appearance connector end V is none v v create edge rules vlis z yellow node appearance node fill color Y create node rules Add Mapping Rules 24 woes amp Node and Line Mappings Node Properties Edge Properties Pathway Selection Get Selected Nodes and Edges is E green wis gt Diamond 8 nodes and 6 edges have been selected selected edge appearance line color v v 7 create edge rules selected node appearance node shape Y v cre

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