SBML model optimisation

Script

import org.sbml.libsbml.*;
import java.sql.*;
import org.sqlite.JDBC;

String DATABASE_NAME = "taverna_sbml";
String databaseURL = "jdbc:sqlite:" + DATABASE_NAME + ".db";

//Set up database
try
{
  //System.loadLibrary("sbmlj");

  driver = "org.sqlite.JDBC";

  Class.forName(driver);
  Connection conn = DriverManager.getConnection(databaseURL);
  Statement stat = conn.createStatement();

  //Create compartment table
  stat.executeUpdate("drop table if exists compartment;");
  stat.executeUpdate("create table compartment (id, name, outside, sboTerm, goId);");

  //Create species table for holding metabolite and enzyme data
  stat.executeUpdate("drop table if exists species;");
  stat.executeUpdate("create table species (id, name, compartmentId, sboTerm, chebi, kegg, inchi, sgd, uniprot);");

  //Create reaction table for holding reactants and products
  stat.executeUpdate("drop table if exists reaction;");
  stat.executeUpdate("create table reaction (id, name, sboTerm, subsystem, ec, pubmed, tag);");

  //Create reactionspecies table for holding associations between species and reaction
  stat.executeUpdate("drop table if exists reactionspecies;");
  stat.executeUpdate("create table reactionspecies (reactionId, speciesId, stoichiometry, role);");

  //====================
  //For storing kinetics
  //====================

  //Create kineticlaw table
  stat.executeUpdate("drop table if exists kineticlaw;");
  stat.executeUpdate("create table kineticlaw (id, reactionId, formula, generalId, reversible);");

  //Create kineticlawvariable table
  stat.executeUpdate("drop table if exists kineticlawvariable;");
  stat.executeUpdate("create table kineticlawvariable (kineticLawId, variableId, relFormula);");

  //Create parameter table
  stat.executeUpdate("drop table if exists parameter;");
  stat.executeUpdate("create table parameter (id INTEGER PRIMARY KEY AUTOINCREMENT, name, role, type, kineticLawId, speciesId, comment, stValue, stDeviation, endValue, unitId);");

  //Create unit table
  stat.executeUpdate("drop table if exists unit;");
  stat.executeUpdate("create table unit (id, description, sbmlUnitId, comment);");

  //Create sbmlunit table
  stat.executeUpdate("drop table if exists sbmlunit;");
  stat.executeUpdate("create table sbmlunit (id, kind, exponent, scale, multiplier, offset);");

  //Create envkineticlaw table
  stat.executeUpdate("drop table if exists envkineticlaw;");
  stat.executeUpdate("create table envkineticlaw (kineticLawId, environDataId);");

  //Create environmentaldata table
  stat.executeUpdate("drop table if exists environmentaldata;");
  stat.executeUpdate("create table environmentaldata (id, stValue, endValue, bufferDescription, description, unitId, comment);");

  //============================
  //Load compartments into table
  //============================
  PreparedStatement prep1 = conn.prepareStatement("insert into compartment values (?, ?, ?, ?, ?);");
  SBMLReader reader = new SBMLReader();
  SBMLDocument doc  = reader.readSBMLFromString(sbml);
  Model m = doc.getModel();
  System.out.println("Model id: " + m.getId());

  ListOfCompartments compList = m.getListOfCompartments();
  for (int i = 0; i < compList.size(); i++)
  {
    Compartment comp = (Compartment) compList.get(i);
    String id = comp.getId();
    String name = comp.getName();
    String outside = comp.getOutside();
    int sboTerm = comp.getSBOTerm();

    String goId = "";
    for (int x = 0; x < comp.getNumCVTerms(); x++)
    {
      CVTerm term = comp.getCVTerm(x);
      XMLAttributes att = term.getResources();
      for (int y = 0; y < att.getLength(); y++)
      {
        String uri = att.getValue(y);
        if (uri.contains("obo.go"))
        {
          goId = uri;
        }
      }
    }

    prep1.setString(1, id);
    prep1.setString(2, name);
    prep1.setString(3, outside);
    prep1.setInt(4, sboTerm);
    prep1.setString(5, goId);
    prep1.addBatch();
  }

  //============================
  //Load species into table
  //============================
  PreparedStatement prep = conn.prepareStatement("insert into species values (?, ?, ?, ?, ?, ?, ?, ?, ?);");
  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();
    String compartment = sp.getCompartment();
    int sboTerm = sp.getSBOTerm();
    if (sboTerm == -1)
      sboTerm = 0;

    String chebi = "";
    String kegg = "";
    String inchi = "";
    String sgd = "";
    String uniprot = "";

    try
    {
      XMLNode node = sp.getAnnotation();
      XMLNode node2 = node.getChild(0);
      XMLNode node3 = node2.getChild(0);
      if(XMLNode.convertXMLNodeToString(node3).contains("InChI"))
        inchi = node3.getCharacters();
    } catch (NullPointerException e) //Catch metabolites with no inchi codes
    {
      System.err.println("No inchi code");
      inchi = "";
    }

    StringBuffer uniprotSb = new StringBuffer();
    for (int x = 0; x < sp.getNumCVTerms(); x++)
    {
      CVTerm term = sp.getCVTerm(x);
      XMLAttributes att = term.getResources();
      for (int y = 0; y < att.getLength(); y++)
      {
        String uri = att.getValue(y);
        if (uri.contains("chebi"))
        {
          chebi = uri;
        } else if (uri.contains("kegg"))
        {
          kegg = uri;
        } else if (uri.contains("sgd"))
        {
          sgd = uri;
        } else if (uri.contains("uniprot"))
        {
          uniprotSb.append("," + uri);
        }
      }
    }

    prep.setString(1, id);
    prep.setString(2, name);
    prep.setString(3, compartment);
    prep.setInt(4, sboTerm);
    prep.setString(5, chebi);
    prep.setString(6, kegg);
    prep.setString(7, inchi);
    prep.setString(8, sgd);
    uniprot = uniprotSb.toString();
    uniprot = uniprot.replaceFirst(",", "");
    prep.setString(9, uniprot);
    prep.addBatch();
  }

  //============================
  //Load reactions into table
  //============================
  PreparedStatement prep4 = conn.prepareStatement("insert into reaction values (?, ?, ?, ?, ?, ?, ?);");
  PreparedStatement prep2 = conn.prepareStatement("insert into reactionspecies values (?, ?, ?, ?);");
  PreparedStatement prep5 = conn.prepareStatement("insert into kineticlaw values (?, ?, ?, ?, ?);");
  PreparedStatement prep6 = conn.prepareStatement("insert into parameter values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);");
  ListOfReactions reactions = m.getListOfReactions();
  for (int i = 0; i < reactions.size(); i++)
  {
    Reaction r = (Reaction) reactions.get(i);
    String id = r.getId();
    String name = r.getName();
    int sboTerm = r.getSBOTerm();

    //Sort out subsystem
    String anno = r.getNotesString();
    int start = anno.indexOf("
");
    int end = anno.indexOf("
");

    //Sort out pubmed annotations for reaction
    String ec = "";
    String pubmed = "";
    for (int x = 0; x < r.getNumCVTerms(); x++)
    {
      CVTerm term = r.getCVTerm(x);
      XMLAttributes att = term.getResources();
      for (int y = 0; y < att.getLength(); y++)
      {
        uri = att.getValue(y);
        if (uri.contains("ec-code"))
        {
          ec = uri;
        } else if (uri.contains("pubmed"))
        {
          pubmed = uri;
        }
      }
    }

    prep4.setString(1, id);
    prep4.setString(2, name);
    prep4.setInt(3, sboTerm);
    prep4.setString(4, subsystem);
    prep4.setString(5, ec);
    prep4.setString(6, pubmed);
    prep4.setString(7, "");
    prep4.addBatch();

    ListOfSpeciesReferences reactants = r.getListOfReactants();
    for (int x = 0; x < reactants.size(); x++)
    {
      SpeciesReference spRef = (SpeciesReference) reactants.get(x);
      species = spRef.getSpecies();
      prep2.setString(1, id);
      prep2.setString(2, species);
      prep2.setDouble(3, spRef.getStoichiometry());
      prep2.setString(4, "reactant");
      prep2.addBatch();
    }

    ListOfSpeciesReferences products = r.getListOfProducts();
    for (int x = 0; x < products.size(); x++)
    {
      SpeciesReference spRef = (SpeciesReference) products.get(x);
      species = spRef.getSpecies();
      prep2.setString(1, id);
      prep2.setString(2, species);
      prep2.setDouble(3, spRef.getStoichiometry());
      prep2.setString(4, "product");
      prep2.addBatch();
    }

    ListOfSpeciesReferences modifiers = r.getListOfModifiers();
    for (int x = 0; x < modifiers.size(); x++)
    {
      ModifierSpeciesReference spRef = (ModifierSpeciesReference) modifiers.get(x);
      species = spRef.getSpecies();
      prep2.setString(1, id);
      prep2.setString(2, species);
      prep2.setDouble(3, 0);
      prep2.setString(4, "modifier");
      prep2.addBatch();
    }

    //Load kinetic law data
    KineticLaw kl = r.getKineticLaw();
    String formula = kl.getFormula();
    String klId = "kl_" + r.getId();
    prep5.setString(1, klId);
    prep5.setString(2, r.getId());
    prep5.setString(3, formula);
    prep5.setString(4, "");
    prep5.setString(5, "");
    prep5.addBatch();

    //Load Parameter data from reaction
    ListOfParameters params = kl.getListOfParameters();
    for(int x = 0; x < params.size(); x++)
    {
      Parameter p = params.get(x);
      System.out.println(p.getId());
      prep6.setString(2, p.getId());
      prep6.setString(3, "");
      prep6.setString(4, "reaction");
      prep6.setString(5, klId);
      prep6.setString(6, p.getId());
      prep6.setString(6, "");
      String stValue = Double.toString(p.getValue()); 
      prep6.setString(7, "");
      prep6.setString(8, stValue);
      prep6.setString(9, "");
      prep6.setString(10, "");
      prep6.addBatch();
    }
  }

  //Load arbitary parameters from model
  ListOfParameters params = m.getListOfParameters();
  for(int x = 0; x < params.size(); x++)
  {
    Parameter p = params.get(x);
    System.out.println(p.getId());
    prep6.setString(2, p.getId());
    prep6.setString(3, "");
    prep6.setString(4, "arbitraryVariable");
    prep6.setString(5, "");
    prep6.setString(6, p.getId());
    prep6.setString(6, "");
    String stValue = Double.toString(p.getValue()); 
    prep6.setString(7, "");
    prep6.setString(8, stValue);
    prep6.setString(9, "");
    prep6.setString(10, "");
    prep6.addBatch();
  }

  conn.setAutoCommit(false);
  prep1.executeBatch();
  prep.executeBatch();
  prep2.executeBatch();
  prep4.executeBatch();
  prep5.executeBatch();
  prep6.executeBatch();
  conn.setAutoCommit(true);
  conn.close();

} catch (ClassNotFoundException e)
{
  e.printStackTrace();
} catch (SQLException e)
{
  e.printStackTrace();
}

Value

Script

import org.sbml.libsbml.*;

//To hold model species ids
spIds = new ArrayList();

//For output
sb = new StringBuffer();
sb2 = new StringBuffer();

//Extract species ids and names from sbml model
SBMLDocument doc = libsbml.readSBMLFromString(sbml);
Model m = doc.getModel();
ListOfSpecies splist = m.getListOfSpecies();
sb.append("Species in SBML model\n");
for(int i = 0; i < splist.size(); i++)
{
  Species s = splist.get(i);
  sb.append(s.getId() + "\t");
  spIds.add(s.getId());
  sb.append(s.getName() + "\n");
} 
//String out = sb.toString();

//Extract species ids from SBRML file
sb.append("Species in SBRML file\n");
String[] lines = sbrml.split("\n");
for(int x = 0; x < lines.length; x ++)
{
  //Check
  String line = lines[x];
  if(line.contains("compositeValue indexValue"))
  {
    if(line.contains("CHEBI"))
    {
      x = x + 2;
      continue;
    }
    else
    {
      int start = line.indexOf("\"");
      int end = line.lastIndexOf("\"");
      String id = line.substring(start + 1, end);
      if(!spIds.contains(id))
      {
        x = x + 2;
        continue;
      }
      else
      {
	sb2.append(line + "\n");
        continue;
      }
    }
  }
  sb2.append(line + "\n");
}

String out = sb.toString();
String newSbrml = sb2.toString();

Script

import javax.swing.*;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableColumn;
import javax.swing.event.ListSelectionListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.table.AbstractTableModel;

import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.Container;
import java.io.*;
import java.util.Hashtable;
import java.util.ArrayList;
import java.sql.*;


class Parameter
{
  String name;
  double value;
  String type;
  String modelId;
  String parameterId;

  Parameter(String name, String value, String type, String modelId, String parameterId)
  {
    this.name = name;
    this.value = Double.parseDouble(value);
    this.type = type; 
    this.modelId = modelId; 
    this.parameterId = parameterId;
  }

  String getName()
  {
    return name;
  }

  String setName(String name)
  {
    this.name = name;
  }

  double getValue()
  {
    return value;
  }

  String setValue(String value)
  {
    this.value = Double.parseDouble(value);
  }

  String getType()
  {
    return type;
  }

  String setType(String type)
  {
    this.type = type;
  }

  String getModelId()
  {
    return this.modelId;
  }

  String setModelId(String modelId)
  {
    this.modelId = modelId;
  }

  String getParameterId()
  {
    return parameterId;
  }

  String setParameterId(String parameterId)
  {
    this.parameterId = parameterId;
  }
}

/**
 * New table model for storing parameter data
 */
class MyTableModel extends AbstractTableModel
{
  //Set up data for table
  String[] colnames = {"Parameter name", "Value", "Lower bound", "Upper bound", "Affected experiment", "Object type", "Model Id"};
  int numrows = params.size();
  int numcols = 7;
  data = new String[numrows][numcols];
  //Iterate thru parameters
  for(int i = 0; i < params.size(); i++)
  {
    p = params.get(i);
    data[i][0] = p.getName();
    double value = p.getValue();
    data[i][1] = Double.toString(value);
    if(p.getType().equals("arbitraryVariable"))
    {
      //Lower bound value
      data[i][2] = Double.toString(value / 4);
      //Upper bound value
      data[i][3] = Double.toString(value * 4);
      data[i][5] = "arbitraryVariable";
    }
    else if(p.getType().equals("reaction"))
    {
      //Lower bound value
      data[i][2] = Double.toString(value / 1000000);
      //Upper bound value
      data[i][3] = Double.toString(value * 1000000);
      data[i][5] = "reaction";
    }
    //Affected experiment
    data[i][4] = "all";
    //ModelId
    data[i][6] = p.getModelId();
  }

  public int getColumnCount()
  {
    return colnames.length;
  }

  public int getRowCount()
  {
    return data.length;
  }

  public String getColumnName(int col)
  {
    return colnames[col];
  }

  public Object getValueAt(int row, int col)
  {
    return data[row][col];
  }

  /*
   * JTable uses this method to determine the default renderer/
   * editor for each cell.  If we didn't implement this method,
   * then the last column would contain text ("true"/"false"),
   * rather than a check box.
   */
  public Class getColumnClass(int c)
  {
    return getValueAt(0, c).getClass();
  }

  /*
   * Don't need to implement this method unless your table's
   * editable.
   */
  public boolean isCellEditable(int row, int col)
  {
    //Note that the data/cell address is constant,
    //no matter where the cell appears onscreen.
    if (col < 2)
      return false;
    else
      return true;
  }

  /*
   * Don't need to implement this method unless your table's
   * data can change.
   */
  public void setValueAt(Object value, int row, int col)
  {
    data[row][col] = value;
    fireTableCellUpdated(row, col);
  }

  public String[][] getData()
  {
    return data;
  }
}

String DATABASE_NAME = "taverna_sbml";
String databaseURL = "jdbc:sqlite:" + DATABASE_NAME + ".db";

//Get parameter data from database
params = new ArrayList();
try
{
  driver = "org.sqlite.JDBC";
  Class.forName(driver);
  Connection conn = DriverManager.getConnection(databaseURL);
  Statement stat = conn.createStatement();
  
  sql = "select name, stValue, type, kineticLawId from parameter;";
  ResultSet rs = stat.executeQuery(sql);
  
  while (rs.next())
  {
    name = rs.getString(1);
    stValue = rs.getString(2);
    type = rs.getString(3);
    kineticLawId = rs.getString(4);
    System.out.println(kineticLawId);
    if(kineticLawId.equals(""))
      modelId = name;
    else
      modelId = kineticLawId.replaceFirst("kl_", "");

    if(type.equals("reaction"))    
      parameterId = name;
    else
      parameterId = "";
    
    p = new Parameter(name, stValue, type, modelId, parameterId);
    params.add(p);
  }
  rs.close();
  conn.close();

}
catch (ClassNotFoundException e)
{
  e.printStackTrace();
}
catch (SQLException e)
{
  e.printStackTrace();
}

/**
 * Class representing the SetFitItemsAndMethod XML document
 */

class Document
{
  String contents;

  Document()
  {
    this.contents = "";
  }

  synchronized void setContents(String data)
  {
    this.contents = data;
    notifyAll();
  }

  synchronized String getContents()
  {
    while (contents.equals(""))
    {
      try
      {
        wait();
      }
      catch (InterruptedException e)
      {
        e.printStackTrace();
      }
    }
    return contents;
  }
}


/**
 * Class representing the GUI for selecting the values to be
 * processed by the remainder of the workflow.
 */
MultipleSelectWorkerGUI(Document doc)
{
  JTable table;
  DefaultTableModel tablemodel;
  JSplitPane splitPane;
  JTextArea expCondition;
  JList list;
  JButton submitButton;

  Document doc;
  
  void init()
  {
    super.frame = new JFrame("Select data for downstream analysis");
    super.frame.setLocationRelativeTo(null); //Place window in centre
    pane = new JPanel(); 
    super.frame.getContentPane().add(pane); 
    pane.setLayout(new BoxLayout(pane, BoxLayout.PAGE_AXIS));
    this.doc = doc;

    table = new JTable(new MyTableModel());

    //Detect row clicked
    rowListener = new ListSelectionListener()
    {
      void valueChanged(ListSelectionEvent event)
      {
        if (event.getValueIsAdjusting())
        {
          return;
        }
        //Selected row changed, do something...
        showReactionInstIds();
      }
    };

    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
    DefaultListSelectionModel lst = table.getSelectionModel();
    lst.addListSelectionListener(rowListener);

    JScrollPane tableScrollPane = new JScrollPane(table);
    pane.add(tableScrollPane);

    //Create a panel
    JPanel buttonPane = new JPanel();
    submitButton = new JButton("Submit");
    submitButton.setActionCommand("submit");
    submitButton.addActionListener(this);
    submitButton.setEnabled(false);
    buttonPane.add(submitButton);
    buttonPane.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    pane.add(submitButton);

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

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

    //New
    String command = e.getActionCommand();

    tmodel = table.getModel();
    data = tmodel.getData();

    if("submit".equals(command))
    {
      //Generate setFitItem XML document
      StringBuffer sb = new StringBuffer();
      //Set userId and resourceId
      sb.append("\n");
      sb.append("\t" + resourceId + "\n");
      sb.append("\t" + userId + "\n");
      sb.append("\t\n");

      for(int i = 0; i < data.length; i++)
      {
        sb.append("\t\t\n");
         
        if(data[i][5].equals("reaction"))
        {
          sb.append("\t\t\t\n");
          sb.append("\t\t\t\t" + data[i][6] + "\n");
          sb.append("\t\t\t\t" + data[i][0] + "\n");
          sb.append("\t\t\t\n");
          sb.append("\t\t\t" + data[i][4] + "\n");
          sb.append("\t\t\n");
        }

        if(data[i][5].equals("arbitraryVariable"))
        {
          sb.append("\t\t\t\n");
          sb.append("\t\t\t\t" + data[i][0] + "\n");
          sb.append("\t\t\t\n");
          sb.append("\t\t\t" + data[i][4] + "\n");
          sb.append("\t\t\n");
        }
      }

      sb.append("\t\t\n");
      sb.append("\t\t\t\n");
      sb.append("\t\t\t\t200\n");
      sb.append("\t\t\t\t1.0E-6\n");
      sb.append("\t\t\t\n");
      sb.append("\t\t\n");

/*
      sb.append("\t\t\n");
      sb.append("\t\t\t\n");
      sb.append("\t\t\t\t200\n");
      sb.append("\t\t\t\t20\n");
      sb.append("\t\t\t\t1\n");
      sb.append("\t\t\t\t0\n");
      sb.append("\t\t\t\n");
      sb.append("\t\t\n");
*/
      sb.append("\t\n");
      sb.append("\n");

      this.document.setContents(sb.toString());
      super.frame.dispose();         
    }
  }

  void showReactionInstIds()
  {
    for (int c : table.getSelectedRows())
    {
      rowSelected = "Row selected: " + c;
      row = c;
      tmodel = table.getModel();
      System.out.println("New row clicked");
      submitButton.setEnabled(true);
    }
  }

  init(); 
  return this; 
}

/**
 * Wrapper for MultipleSelectWorkerGUI
 */ 
class WorkerWrapper extends Thread
{
  Document document; 

  WorkerWrapper(Document document)
  {
    this.document = document;
  }

  void run()
  {
    msw = MultipleSelectWorkerGUI(this.document);
  }
}

document = new Document();
wrapper = new WorkerWrapper(document);
wrapper.start();
String setFitItemsAndMethodXML = document.getContents();