/**
     * Example 5a
     * Metabolic Graph : each node represents a metabolite or a reaction
     * build the grah, export it in graphml and draw it in a new window
     * mySQL is required
     */
    public static void TutorialEx5a(String myOrganism, int max) {
        String keySession = new String("cyclone");
        
        //Structure to store the tempory graph
        ArrayList> myPseudoGraph = new ArrayList>(); 
        
        //Ask for a DataAccessObject (Dao) to manipulate the generalized-reactions
        GeneralizedReactionsDao rdao = new GeneralizedReactionsDao(keySession);
        
        //Get all Reactions
        List myRxns = rdao.getAllObjectsByInstance(myOrganism,"|Reactions|");     
        //List myObNodes = new ArrayList();     
        // myObNodes.addAll(rdao.getAllObjectsByInstance(orgid,"|Reactions|"));
        
        int i=0;  
        //For each reaction, extract the left and right metabolites
        for(GeneralizedReactions myRxn  : myRxns){    
            System.out.println("Dealing with "+myRxn.getFrameId());
            List leftts = rdao.getValueList(myRxn.getLeftt());
            for(String metaboliteFrame : leftts){
                ArrayList myTmpEdge = new ArrayList();
                myTmpEdge.add(metaboliteFrame);
                myTmpEdge.add(myRxn.getFrameId());
                myPseudoGraph.add(myTmpEdge);
            }
            
            List rightts = myRxn.getRightt();
            for(Rightt metabolite : rightts){
                ArrayList myTmpEdge = new ArrayList();
                myTmpEdge.add(myRxn.getFrameId());
                myTmpEdge.add(metabolite.getValue());
                myPseudoGraph.add(myTmpEdge);
            }
            if(i==max){break;}else{i++;}
        }      
        
        //Export it in Graphml format
        Graphml myGraph2 = GraphmlServices.buildGraphML(max,"MetabolismNetwork of "+myOrganism,myPseudoGraph);
        String filexml2 = GraphmlServices.export2Xml(myGraph2,"Data/Graphs/GraphM
        L/"+myOrganism+"_metabolicnetwork"+(new Date()).getTime()+".xml");
        
        //Display it in a window using jung api
        GraphmlServices.displayGraph(filexml2);
    }

A Flash tutorial illustrates this step.
Flash Tutorial

Below is an extract of the output GraphML file corresponding to the Ecoli metabolic graph:

<?xml version"1.0" encoding"UTF-8" standalone"yes"?>
<graphml xmlns"http://graphml.graphdrawing.org/xmlns/1.0rc">
    <desc>MetabolismNetwork of Ecoli</desc>
    <graph parse.edges"5526" parse.nodes"2716" parse.order"free" edgedefault"directed" id"MetabolismNetwork of Ecoli">
        <node id"ACYL-ACP"/>
        <node id"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN"/>
        <edge id"ACYL-ACP_1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN" source"ACYL-ACP" target"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN"/>
        <node id"ACYL-SN-GLYCEROL-3P"/>
        <edge id"ACYL-SN-GLYCEROL-3P_1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN" source"ACYL-SN-GLYCEROL-3P" target"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN"/>
        <node id"ACP"/>
        <edge id"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN_ACP" source"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN" target"ACP"/>
        <node id"L-PHOSPHATIDATE"/>
        <edge id"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN_L-PHOSPHATIDATE" source"1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN" target"L-PHOSPHATIDATE"/>
        <node id"GLUCONATE"/>
        <node id"1.1.1.215-RXN"/>
        <edge id"GLUCONATE_1.1.1.215-RXN" source"GLUCONATE" target"1.1.1.215-RXN"/>

This code will display a graph using the Jung API as shown below

    /**
     * Example 5b
     * Transcriptional Regulation Interaction Graph: each node represents a gene
     * export the graph into Cytoscape format
     * mySQL is required
     */
    public static void TutorialEx5b(String myOrganism, int max) {
        String keySession = new String("cyclone");
        Regulation myRegulation = TranscriptionalRegulationCreator.getRegulation( keySession ,  myOrganism, max);
        //print in the console
        myRegulation.display();
        
        //Export it in Cytoscape format (SIF, NA)
        myRegulation.toCytoscape();
        
        //print it for NeMo clusters analysis tool
        //myRegulation.toClusterMatrix();        
    }

    /**
    * Given an organism, this function extracts the metabolic regulation network
    * Foreach enzymaticreaction, extract the metabolites that inhibits/activates the enzyme
    * @param orgid
    * @param keySession
    * @return
     */
   private static Graphml getGraphml(String orgid,String keySession){
       Graphml myGraphml = null;
       ObjectFactory myObjectFactory = new ObjectFactory();
       Graph myGraph = null;
       HashMap myNodes = new HashMap();
       HashMap myEdges = new HashMap();
       try
       {
           myGraphml   = myObjectFactory.createGraphml();
           myGraphml.setDesc("Hard coded desc Ecoli.metabolicRegulation.network.graphml.xml");
           myGraph = myObjectFactory.createGraph();
           myGraph.setId("mr");
           myGraph.setParseOrder(TypeGraphOrderType.FREE);
           myGraph.setEdgedefault(TypeGraphEdgedefaultType.DIRECTED);
           myGraphml.getGraphOrData().add(myGraph);
           Key myKeyNodeType = myObjectFactory.createKey();
           myKeyNodeType.setId("NodeType");
           myKeyNodeType.setFor(TypeKeyForType.NODE);
           myKeyNodeType.setAttrName("nodetype");
           myKeyNodeType.setAttrType(TypeKeyTypeType.STRING);
           myGraphml.getKey().add(myKeyNodeType);
           Key myKeyEdgeType = myObjectFactory.createKey();
           myKeyEdgeType.setId("regulation");
           myKeyEdgeType.setFor(TypeKeyForType.NODE);
           myKeyEdgeType.setAttrName("regulationtype");
           myKeyEdgeType.setAttrType(TypeKeyTypeType.STRING);
            myGraphml.getKey().add(myKeyEdgeType);

       EnzymaticReactionsDao cdao = new EnzymaticReactionsDao(keySession);
       List myEnzymaticReactions = cdao.getListAllObjects(orgid);
       String framerxn;
       String myFrameActivator, myFrameInhibitor;
       int i=0;
       for(EnzymaticReactions myEnzymaticReaction : myEnzymaticReactions){
           framerxn =  ((Reaction)myEnzymaticReaction.getReaction().get(0)).getValue();
           List myActivators = myEnzymaticReaction.getActivatorsAll();
           for(ActivatorsAll myActivatorsAll :myActivators){
                   myFrameActivator = myActivatorsAll.getValue();
                   Node myNodeRxn = getNode(myGraph,framerxn,myNodes, myKeyNodeType, "rxn");
                   Node myNodeMet = getNode(myGraph,myFrameActivator,myNodes, myKeyNodeType, "metabolite");
                   String edgeName = myNodeMet.getId()+"_"+myNodeRxn.getId();
                   Edge myEdge = getEdge(myGraph,edgeName,myEdges,myKeyEdgeType,"active");
                   myEdge.setSource(myNodeMet);
                   myEdge.setTarget(myNodeRxn);              
           }                                          
           List myInhibitorsAlls = myEnzymaticReaction.getInhibitorsAll();
           for(InhibitorsAll myInhibitorsAll :myInhibitorsAlls){                 
                myFrameInhibitor = myInhibitorsAll.getValue();
                Node myNodeRxn = getNode(myGraph,framerxn,myNodes, myKeyNodeType, "rxn");
                Node myNodeMet = getNode(myGraph,myFrameInhibitor,myNodes, myKeyNodeType, "metabolite");
                String edgeName = myNodeMet.getId()+"_"+myNodeRxn.getId();
                Edge myEdge = getEdge(myGraph,edgeName,myEdges,myKeyEdgeType,"inhibe");
                myEdge.setSource(myNodeMet);
                myEdge.setTarget(myNodeRxn);                 }
                    // if(i==10){ break;}else{i++;}
           }
           myGraph.setParseNodes(BigInteger.valueOf(myNodes.size()));
           myGraph.setParseEdges(BigInteger.valueOf(myEdges.size()));
           System.out.println(myEdges.size());
       } catch (JAXBException e)
       {
           // TODO Auto-generated catch block
           e.printStackTrace();
       }
       return myGraphml;
   }

    
    /**
     * Example 5c
     * Full Graph: 
     * each node can represent a gene, a reaction or a metabolite,
     * each link can represents transcriptional regulation, metabolite regulation, metabolite reaction
     * mySQL is required
     */
    public static void TutorialEx5c(String myOrganism, int max) {      
        FullNetwork.completeNetwork(myOrganism,  max);  
    }