Compartmental models of growing neurites (Graham and van Ooyen 2004)

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Simulator for models of neurite outgrowth. The principle model is a biophysical model of neurite outgrowth described in Graham and van Ooyen (2004). In the model, branching depends on the concentration of a branch-determining substance in each terminal segment. The substance is produced in the cell body and is transported by active transport and diffusion to the terminals. The model reveals that transport-limited effects may give rise to the same modulation of branching as indicated by the stochastic BESTL model. Different limitations arise if transport is dominated by active transport or by diffusion.
1 . Graham BP, van Ooyen A (2004) Transport limited effects in a model of dendritic branching. J Theor Biol 230:421-32 [PubMed]
2 . Graham BP, van Ooyen A (2006) Mathematical modelling and numerical simulation of the morphological development of neurons. BMC Neurosci 7 Suppl 1:S9 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s):
Gap Junctions:
Simulation Environment: Java;
Model Concept(s): Development;
Implementer(s): Graham, Bruce [B.Graham at];

General purpose "help" text displayer

BPG 20-11-05

import java.awt.*;
import java.awt.event.*;

public class HelpWindow extends Frame implements ActionListener {

	private Button closeB;
	public HelpWindow() {
		// Frame properties
        setTitle("Neurite User Guide");
        setSize(700, 550);
        setLocation(100, 100);
        setLayout(new BorderLayout());

        // Read "help" text from file
        BufferedReader inFile;
        String text = "";
		try {

  	      inFile = new BufferedReader(new FileReader("readme.txt"));
  	      String line = inFile.readLine();
  	      text = line;
  	      while ((line = inFile.readLine()) != null) {
  	      	text = text.concat("\n");
  	      	text = text.concat(line);
  	      // Close the file
  		catch(Exception ex) {
  			System.out.println("Error: Unable to open or read the help file.");
	    // Create text pane to display "help"  
        TextArea pane = new TextArea(text, 500, 1, TextArea.SCROLLBARS_VERTICAL_ONLY);
        pane.setBounds(5, 5, 5, 5);
	    // Set invisible cursor back to first position in pane to ensure 
	    // that the first line is displayed first to user
  		add(pane, BorderLayout.CENTER);
  		// "Close" button
  		closeB = new Button("Close Window");
  		Panel buttonP = new Panel();
  		  		add(buttonP, BorderLayout.SOUTH);
  		// display the frame window

	public void actionPerformed(ActionEvent e) {