Copasi time simulation of SBML model

Value

Script

import java.util.Iterator;
import java.util.List;
import javax.xml.namespace.NamespaceContext;
import javax.xml.parsers.*;
import javax.xml.xpath.*;
import org.w3c.dom.Document;
import org.apache.xpath.NodeSet;
import java.io.*;
import org.w3c.dom.*;
import org.xml.sax.InputSource;
import org.apache.xpath.NodeSet;


DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
domFactory.setNamespaceAware(true); // never forget this!
DocumentBuilder builder = domFactory.newDocumentBuilder();
ByteArrayInputStream bs = new ByteArrayInputStream(sbrml.getBytes());
Document doc = builder.parse(bs);

NamespaceContext ctx = new NamespaceContext()
{
  public String getNamespaceURI(String prefix)
  {
    String uri;
    if (prefix.equals("ns1"))
      uri = "http://www.sbrml.org/sbrml/level1/version1";
    else
      uri = null;
  
    return uri;
  }

  //Dummy implementation - not used!
  public Iterator getPrefixes(String val)
  {
    return null;
  }

  //Dummy implemenation - not used!
  public String getPrefix(String uri)
  {
    return null;
  }
};

//Get all time frames
String xpathStr1 = "/ns1:sbrml/ns1:operations/ns1:operation/ns1:result/ns1:resultComponent/ns1:dimension/ns1:compositeValue/@indexValue";

//Get all species names
String xpathStr2 = "/ns1:sbrml/ns1:operations/ns1:operation/ns1:result/ns1:resultComponent/ns1:dimension/ns1:compositeValue[@indexValue='0']/ns1:compositeValue/@indexValue";

XPathFactory xpathFact = XPathFactory.newInstance();
XPath xpath = xpathFact.newXPath();
xpath.setNamespaceContext(ctx);
Object result = xpath.evaluate(xpathStr1, doc, XPathConstants.NODESET);
NodeList nodes = (NodeList) result;
//Sort out output
StringBuffer sb = new StringBuffer();
//sb.append("Species");
ArrayList timeframes = new ArrayList();
for (int i = 0; i < nodes.getLength(); i++)
{
  String time = nodes.item(i).getNodeValue();
  timeframes.add(time);
  sb.append(time);
  if(i == nodes.getLength() - 1)
    sb.append("\n");
  else
    sb.append(",");
}

//Use species names in sbrml
String[] lines = species.split("\n");
Hashtable ht = new Hashtable();
for(int x = 0; x < lines.length; x++)
{
  String[] tokens = lines[x].split(";");
  String spId = tokens[0];
  String name = tokens[1];
  if(name.equals("Nicotinamide adenine dinucleotide - reduced"))
    name = "NADH";
  else if(name.equals("Nicotinamide adenine dinucleotide"))
    name = "NAD";
  ht.put(spId, name);
}

Object result = xpath.evaluate(xpathStr2, doc, XPathConstants.NODESET);
NodeList nodes = (NodeList) result;
for (int i = 0; i < nodes.getLength(); i++)
{
  String species  = nodes.item(i).getNodeValue();
  String speciesName = ht.get(species);
  if(!selectedSpeciesNames.contains(speciesName))
    continue;
  else
  {
    sb.append("\"" + speciesName + "\"");
    //Iterate
    for(int x = 0; x < timeframes.size(); x++)
    {
      String timeFrame = timeframes.get(x);
      //Get concentration values
      String xpathStr3 = "/ns1:sbrml/ns1:operations/ns1:operation/ns1:result/ns1:resultComponent/ns1:dimension/ns1:compositeValue[@indexValue='" + timeFrame + "']/ns1:compositeValue[@indexValue='" + species + "']/ns1:tuple/ns1:atomicValue[1]";
      String data2 = xpath.evaluate(xpathStr3, doc);
      sb.append("," + data2);
    }
    sb.append("\n");
  }
}

//Output
String output = sb.toString();

Script

#Initialise output of png image
png(graph_image);
#Read in csv data from previous taverna activity
data <- read.table(file=csv,head=TRUE,sep=",");
#transpose data
tdata <- t(data);
#Plot all species concentrations against time
matplot(tdata,axes=F,frame=T,type="l", col= 1:ncol(tdata), ylab="Concentration", xlab="Time"); 
#Add title
title("Copasi time course simulation");
# put numerical annotations at the tickmarks in y-axis; 
axis(2);
#Remove Xs from row name strings
rnames <- rownames(tdata);
for (i in 1:length(rnames)) #Loop thru rows in x object
{
  rnames[i] <- substr(rnames[i], 2, nchar(rnames[i]));
}
#Add ticks and time unit values to x axis
axis(1, 1:length(rnames), rnames);
#Add legend for species
legend("bottomright", colnames(tdata), lty = 1:ncol(tdata), col = 1:ncol(tdata), cex = .6);
#Close stream to png image
dev.off();

R Server

Value

Script

import org.sbml.libsbml.*;

//Second output
names = new ArrayList();

SBMLReader reader = new SBMLReader();
SBMLDocument doc  = reader.readSBMLFromString(sbml);
Model m = doc.getModel();

//To hold data
StringBuffer data = new StringBuffer();
  
//Get species ids and names
ListOfSpecies spList = m.getListOfSpecies();
for (int i = 0; i < spList.size(); i++)
{
  Species sp = (Species) spList.get(i);
  String id = sp.getId();
  String name = sp.getName();
  names.add(name);
  data.append(id + ";" + name + "\n");
}

//Output
String species = data.toString();

Script

/**
 * Class representing the selected values of this beanshell processor
 */
class SelectedValues
{
  ArrayList selectedValues;

  SelectedValues()
  {
    selectedValues = new ArrayList();
  }

  synchronized void addToValues(ArrayList values)
  {
    for(int i = 0; i < values.size(); i ++)
      selectedValues.add(values.get(i));

    notifyAll();
  }

  synchronized ArrayList getValues()
  {
    while (selectedValues.size() == 0)
    {
      try
      {
        wait();
      }
      catch (InterruptedException e)
      {
        e.printStackTrace();
      }
    }

    return selectedValues;
  }
}

/**
 * Class representing the GUI for selecting the values to be
 * processed by the remainder of the workflow.
 */
MultipleSelectWorkerGUI(ArrayList input, SelectedValues values)
{
  JList list;
  DefaultListModel listModel;
  final String submitString = "Submit";
  JButton submitButton;
  int[] accessions;
  SelectedValues selectedValues;
  ArrayList inputdata;
  

  void init()
  {
    super.frame = new JFrame("Select data for downstream analysis");
    //Place window in centre of the screen
    super.frame.setLocationRelativeTo(null);
    pane = new JPanel(); 
    super.frame.getContentPane().add(pane); 
    pane.setLayout(new BorderLayout()); 

    // Set up input data available for selection
    listModel = new DefaultListModel();
    for (int i = 0; i < input.size(); i++)
      listModel.addElement(input.get(i));
    
    selectedValues = values;

    //Create the list and put it in a scroll pane
    list = new JList(listModel);
    list.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
    list.setSelectedIndex(0);
    list.addListSelectionListener(this);
    list.setVisibleRowCount(10);
    list.setSize(800,500);
    list.setFixedCellHeight(20);

    JScrollPane listScrollPane = new JScrollPane(list);

    submitButton = new JButton(submitString);
    submitButton.setActionCommand(submitString);
    submitButton.addActionListener(this);

    //Create a panel
    JPanel buttonPane = new JPanel();
    buttonPane.add(submitButton);
    buttonPane.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));

    pane.add(listScrollPane, BorderLayout.CENTER);
    pane.add(buttonPane, BorderLayout.PAGE_END);

    //frame.setSize(800,500);
    frame.setVisible(true); 
    frame.pack(); 
  }

  //This method is required by ListSelectionListener.
  void valueChanged(ListSelectionEvent e)
  {
    if (!e.getValueIsAdjusting())
    {
      if (list.getSelectedIndex() == -1)
      {
        //No selection so disable fire button
        submitButton.setEnabled(false);
      }
      else
      {
        //Selection made so enable the fire button.
        submitButton.setEnabled(true);
      }
    }

  }

  // This method is called only if there is a valid selection
  void actionPerformed(ActionEvent e)
  {
    ArrayList al = new ArrayList();

    if (list.getSelectedIndices().length == 0)
    {
      // Nothing selected so disable firing
      submitButton.setEnabled(false);
    }
    else
    {
      selectedItems = list.getSelectedIndices();
      //System.out.println(selectedItems);
      
      for(int i = 0; i < selectedItems.length; i++)
      {
        String str = listModel.elementAt(selectedItems[i]);
        al.add(str);
      }
      
      selectedValues.addToValues(al);
      super.frame.dispose();

    }
  }

  init(); 
  return this; 
}

/**
 * Wrapper for MultipleSelectWorkerGUI
 */ 
class WorkerWrapper extends Thread
{
  SelectedValues selectedValues;
  ArrayList inputdata;

  WorkerWrapper(ArrayList input, SelectedValues v)
  {
    inputdata = inputList;
    selectedValues = v;
  }

  void run()
  {
    msw = MultipleSelectWorkerGUI(inputdata, selectedValues);
  }
}


sv = new SelectedValues();
wrapper = new WorkerWrapper(inputList, sv);
wrapper.start();
outputList = sv.getValues();