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https://github.com/intermine/intermine
A powerful open source data warehouse system
https://github.com/intermine/intermine
api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices
Last synced: about 4 hours ago
JSON representation
A powerful open source data warehouse system
- Host: GitHub
- URL: https://github.com/intermine/intermine
- Owner: intermine
- License: other
- Created: 2012-07-02T10:25:18.000Z (about 12 years ago)
- Default Branch: dev
- Last Pushed: 2023-12-03T01:10:28.000Z (10 months ago)
- Last Synced: 2024-09-19T14:08:47.585Z (5 days ago)
- Topics: api, bioinformatics, biology, clojure, clojurescript, data-visualisation, data-visualization, data-warehouse, genetics, genomics, java, lgplv3, open-source, opensource, perl, postgresql, python, tomcat, tomcat8, webservices
- Language: Java
- Homepage: http://intermine.org
- Size: 636 MB
- Stars: 253
- Watchers: 18
- Forks: 349
- Open Issues: 221
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE-OF-CONDUCT.md
- Support: SUPPORT.md
Awesome Lists containing this project
README
InterMine
============
Master: [](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
Dev: [](https://github.com/intermine/intermine/actions?query=workflow%3A%22InterMine+CI%22)
[](https://github.com/intermine/intermine/releases)
[](https://github.com/intermine/intermine/blob/master/LICENSE)
[](http://depsy.org/package/python/intermine)
[](https://anaconda.org/bioconda/intermine)
[](https://intermine.readthedocs.io/en/latest/?badge=latest)
f
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:
* [FlyMine](https://www.flymine.org)
* [HumanMine](https://www.humanmine.org)
* [MouseMine](http://www.mousemine.org)
* [YeastMine](https://yeastmine.yeastgenome.org)
* [ZebrafishMine](http://zebrafishmine.org)
* [RatMine](http://ratmine.mcw.edu/ratmine/begin.do)
* [TargetMine](http://targetmine.mizuguchilab.org/)
* [ThaleMine](https://apps.araport.org/thalemine)
* [PhytoMine](https://phytozome.jgi.doe.gov/phytomine)
For the full list of InterMines, please see the [registry](http://registry.intermine.org)
For details, please visit: [InterMine Documentation][readthedocs]
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:
[tutorial][tutorial]
3min bootstrap
--------------------------------------
As long as you have the prerequisites installed ([Java][java], [PostgreSQL][psql]), you can get a working data-warehouse and associated web-application by running an automated bootstrap script:
```bash
# For the testmodel
./testmine/setup.sh
```
For a genomic application, with test data from Malaria, see [BioTestMine](https://github.com/intermine/biotestmine)
Docker
--------------------------------------
You can build InterMine using Docker. See https://github.com/intermine/docker-intermine-gradle
Copyright and Licence
------------------------
Copyright (C) 2002-2022 FlyMine
See [LICENSE](LICENSE) file for licensing information.
This product includes software developed by the
[Apache Software Foundation][apache]
InterMine Development Roadmap
-----------------------------
For more information about the upcoming releases, please visit the [InterMine Development Roadmap](http://intermine.org/im-docs/docs/intermine/roadmap/). For the roadmap, please see [here](https://github.com/intermine/intermine/projects/7).
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](https://academic.oup.com/nar/article/42/W1/W468/2435235)
[](https://academic.oup.com/nar/article/42/W1/W468/2435235)
[](http://www.ncbi.nlm.nih.gov/pubmed/24753429)
**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.](http://bioinformatics.oxfordjournals.org/content/28/23/3163.abstract)
[](http://bioinformatics.oxfordjournals.org/content/28/23/3163.abstract)
[](http://www.ncbi.nlm.nih.gov/pubmed/23023984)
See [zotero](https://www.zotero.org/groups/2117194/intermine/) for the full list of InterMine publications.
[travis-badge-master]: https://travis-ci.org/intermine/intermine.svg?branch=master
[ci]: https://travis-ci.org/intermine/intermine
[readthedocs]: http://intermine.readthedocs.org/en/latest
[tutorial]: http://intermine.readthedocs.org/en/latest/get-started/tutorial
[psql]: http://www.postgresql.org
[java]: http://openjdk.java.net
[apache]: http://www.apache.org
[tomcat]: http://tomcat.apache.org/download-70.cgi