Graduate School of Life Sciences

Bioinformatics and computational biology courses

InterMine Data Warehouse Workshop

Richard Smith

Department of Genetics

Date: 16th-17th November 2009
Time: 9.30-5.30
Venue: Genetics Room G12: map
Maximum number: 20
Code: BM06

Bookings are made via the online booking form.

This workshop is intended for software developers aspiring to build a database and web interface with the InterMine software. An example of such a database is FlyMine but InterMine imposes no restriction on the sort of data it can be used to manage. A reasonable grasp of programming in either Java or PERL is essential. Some experience with relational database would also be very useful.

InterMine is an open-source system for integrating biological data from multiple sources and querying it via a web interface and web services. It supports data integration from standard biological formats and makes it easy to add your own data. The web application provides flexible query access and works 'out of the box' for any data model. This allows users to create custom queries, use template queries (web forms to run 'canned' queries), upload and operate on lists of data and analyse lists with interactive graphical or statistical 'widgets'. Queries and lists can be saved in a MyMine account. Queries can also be created with an API and run via RESTful web services.

InterMine was developed to enable FlyMine and is now used in other projects, including modENCODE and three major model organism databases. InterMine is written in Java, all code is freely available under the LGPL license.

The workshop will be hands-on, taking you through all the steps of setting up an InterMine data warehouse. We will integrate some real data using existing InterMine parsers then extend the data model and write parsers in Java/Perl to include some custom data. On the second day we will deploy and configure the web application, add a new widget for analysing lists and learn how to query with web services and the API. This should provide you with the necessary experience to set up your own InterMine system.

An overview of the workshop:

Day 1

* Introduction to InterMine
* Overview of software dependencies: Subversion, Ant, PostgreSQL, Tomcat
* Setting up a new Mine and loading data with existing parsers
* Extending the data model and writing a parser for custom data in Java/Perl
* Importing data from a Chado database
* Performance optimisation

Day 2

* Introduction to the InterMine web application
* Deploying and configuring the web application
* Developing widgets for list analysis
* Using the query API and web services

Please see the web site for more information. If you have any queries about InterMine or the workshop please contact Richard Smith: richard@flymine.org

Prerequisites: You need to be familiar with programming either Java or Perl. A basic knowledge of relational databases would be helpful.

None of our current courses requires you to bring your own computer. However, if you want to bring a laptop and have it online we can arrange access via the University Lapwing wireless service.