InterMine Workshop - October 2008

All of the software that InterMine depends on should already be installed on your workshop computer, see here for details of these.

Some notes about your setup in the training room:

  • each machine has a login with a user name like partXX
  • there is an svn directory in your home directory, this is a symbolic link to a local partition
  • there is a postgres user created with username/password the same as your partXX username

Getting the InterMine code

InterMine code is held in a subversion version control repository. You should check out a copy of the code to your local machine, we will use the workshop-oct-2008 and check it out into a directory called dev in the svn directory on your machine.

From the terminal run: 

% cd ~/svn
% svn co svn://subversion.flymine.org/branches/workshop-oct-2008 dev

Building MalariaMine

In this workshop we will build an example InterMine instance with data from P. falciparum - MalariaMine.

On day one we will learn about building a new Mine, defining the data model and integrating data.

On day two we will release and configure the web application to query this data.

Day One

First we will work through creating the directory structure for MalariaMine, building the database and integrating some data:

Now you will create a new source to add KEGG pathway data to the model and load the data into MalariaMine. You can do this either in Java or Perl:

Finally, we will build a complete MalariaMine database using a build script:

WorkshopDayTwo