Table Of Contents

Previous topic

Data files to integrate

Next topic


This Page

Tutorial - Configure your InterMine webapp!

This tutorial aims to cover the basics of configuring an InterMine webapp.


In general, customisation of InterMine is accomplished by updating the appropriate configuration file and redeploying the webapp. A few features are updated via tagging as well. See Guide to Customising your Web Application for the full documentation on the webapp.


You should have completed the previous tutorial and have successfully deployed the webapp.

This tutorial is intended to give a general idea of what you can customise in InterMine and how to do it. We’re going to go through each section of the webapp and give step by step instructions on how to configure different parts of the page. This is a detailed tutorial and should take you a few hours to complete – however it is not meant to be comprehensive. Where topics aren’t covered, there are links provided for more information. If you have a question that you don’t see answered, try searching the documentation or taking a look at the index. Intermine has an active developer’s Mailing list as well.


You will need to have Tomcat running for this tutorial.

If your webapp is under heavy usage or development, Tomcat may run out of memory. See Tomcat for details on how to update your settings to adjust the amount of memory available to Tomcat.

If Tomcat has run out of memory, it may not shut down correctly. Memory handling seems to have greatly improved with Tomcat 7 however.

General Layout

Each web page in InterMine has the same header and footer. The header contains everything at the top of the page, including the navigation tabs and the keyword search. The footer contains the contact form and InterMine logo.


Header and footer of FlyMine website

Let’s start configuring our mine by updating these common sections of our web application.

Home page

Most everything on the home page is customisable. You can edit the text and set which RSS news feed to use. If you want something very different, you can create and use your own home page.


You can customise the text in the three boxes that appear on the top of the home page. Let’s edit the example given in the middle box marked Analyse.


Three boxes at the top of the home page

Notice the text box already has an example, e.g. X, Y, Z. This is the default example and it’s set by begin.listBox.example in an InterMine properties file,

Add begin.listBox.example to your mine’s Features file and redeploy your webapp to see your changes.

InterMine, bio and mine /webapp

In Intermine there are 3 webapp projects: InterMine, bio and mine. You shouldn’t ever have to change the files in InterMine and bio, you’ll only ever update your mine’s files. When the webapp is compiled, the build system starts with the InterMine webapp project, then merges bio into that. Finally your mine’s webapp is added. The files and properties set in bio override any in the InterMine project. Your mine’s files and properties override any in bio or InterMine.

Therefore when you set begin.listBox.example in your properties file, it overrode the same property set in the InterMine properties file. This will be true of any property.

Use your own

The text and settings are configurable, but you may want a different layout for your home page.

  1. Copy begin.jsp from intermine/webapp into your own webapp directory: MINE_NAME/webapp/resources/webapp/model.
  2. Edit your begin.jsp
  3. Redeploy your webapp to show your change

We saw in the previous section that properties override InterMine properties. The same holds true for JSP pages.

Note: Changes made to the home page, or whichever page you updated, will not be reflected in your custom copy.

See Home page for more details on how to update your home page.