This is the code base for Thalemine, a data warehouse system based on InterMine and used in Araport, the Arabidopsis Information Portal.
ThaleMine enables you to analyze gene and protein data from TAIR, expression and interaction data from BAR, ortholog data from Panther, and more. Use plain text or structured queries to obtain interactive gene and protein reports.
A powerful open source data warehouse system. InterMine allows users to integrate diverse data sources with a minimum of effort, providing powerful web-services and an elegant web-application with minimal configuration. InterMine powers some of the largest data-warehouses in the life sciences, including:
For details, please visit: InterMine Documentation
If you run an InterMine, or use one in your research, in order to improve the chance of continued funding for the InterMine project it would be appreciated if groups that use InterMine or parts of InterMine would let us know.
Getting Started With InterMine
For a guide on getting started with InterMine, please visit: quick start tutorial
# Set up tomcat ./config/download_and_configure_tomcat.sh # For a genomic application, with test data from Malaria ./biotestmine/setup.sh # For the testmodel ./testmodel/setup.sh
This requires that you have all the software dependencies
installed and running with the appropriate user permissions
(postgres, Tomcat, Java SDK). You will need to have set up usernames
and passwords for Tomcat and postgres first, and these can be
provided to the setup scripts as
Copyright and Licence
Copyright (C) 2002-2017 FlyMine
See LICENSE file for licensing information.
This product includes software developed by the Apache Software Foundation
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.
Bioinformatics (2012) 28 (23): 3163-3165.