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InterMine

Master: Build Status: master Dev: Build Status: dev Version License Research software impact Conda

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 the full list of InterMines, please see the registry

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 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

3min bootstrap

As long as you have the prerequisites installed (Java, PostgreSQL), you can get a working data-warehouse and associated web-application by running an automated bootstrap script:

  # 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 (PostgreSQL, Java SDK). You will need to have set up usernames and passwords for PostgreSQL first, and these can be provided to the setup scripts as PSQL_USER.

Copyright and Licence

Copyright (C) 2002-2019 FlyMine

See LICENSE file for licensing information.

This product includes software developed by the Apache Software Foundation

Please cite

InterMine: extensive web services for modern biology.
Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stěpán R, Sullivan J, Micklem G.
Nucleic Acids Res. 2014 Jul; 42 (Web Server issue): W468-72
doi pubmed

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.
doi pubmed

See zotero for the full list of InterMine publications.