Last modified 2 years ago Last modified on 17/11/09 14:32:18

InterMine workshop - November 2009

We will be building MalariaMine - an example InterMine database and web interface with real data sets from the malaria genome (P. falciparum). This will include data:

  • genome sequence and features from PlasmoDB
  • UniProt proteins
  • InterPro protein domains
  • GO annotation
  • publications from pubmed
  • KEGG pathways

Agenda

Day 1 - Monday

  1. Introduction [9:30 - 10:00]
  2. Building the data warehouse [10:00 - 11:00, 11:15 - 12:30]
  3. Lunch [12:30 - 1:30]
  4. Webapp overview (Rachel) [1:30 - 2:30]
  5. Break [2:30 - 3:00]
  6. Launching the webapp [3:00 - 3:20]
  7. GettingStartedWebapp [3:20 - 4:00]

Day 2 - Tuesday

  1. Loading custom data [9:30 - 12:30, break 11:00 - 11:15]
  2. Lunch [12:30 - 1:30]
  3. Customising the web application [1:30 - 3:30]
    • link outs
    • creating a custom data displayer
    • widgets overview
    • exercises
      • updating properties files
      • custom pathway displayer
      • pathway widget
  4. 3:30 - 3:45 break
  5. Web services [3:45 - 4:30]
  6. Further topics [4:30 - 5:00]

Setup

All software required to use InterMine is already installed on these machines. See the dependencies: Prerequisites

There are two links in each user's home directory: svn and tomcat that point to directories on the local machine.

Code checkout

Check out the latest InterMine code to the svn directory: 

> cd svn
> svn co svn://subversion.flymine.org/branches/intermine_0_92 dev

postgres users

There are postgres users set up on each machine, the username and password is the same as the username you are logged in as, e.g. part03/part03

useful pages