GCC2019 has ended
The 2019 Galaxy Community Conference (GCC2019) was held in Freiburg, Germany, 1-8 July.  There was one day of training, three days of mixed meeting and training, and then two to four days of CollaborationFest.  The meeting featured joint & parallel sessions; invited, accepted, and lightning talks; poster and demo sessions; birds-of-a-feather meetups; social events; and training sessions every day.

Thanks to everyone who helped make GCC2019 a success!
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Thursday, July 4 • 15:50 - 17:20
Handling integrated biological data using Python, Jupyter, and InterMine

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This training session has a Gitter channel where preparation instructions are posted, and for class discussion, last minute links, and more.


This tutorial will guide you through loading and analyzing integrated biological data (generally genomic or proteomic data) using InterMine, either via UI or via an API in Python. Topics covered will include automatically generating code to perform queries, customising the code to meet your needs, and automated analysis of sets, e.g gene sets, including enrichment statistics. Skills gained can be re-used in any of the dozens of InterMines available, covering a broad range of organisms and dedicated purposes, from model organisms to plants, drug targets, and mitochondrial DNA.
Users will also be shown how to import and export their gene and protein lists to and from Galaxy to link Galaxy pipelines with InterMine analyses.

  • Basic Python skills are advantageous but not required.
  • A laptop with wifi. Python optional as we can use Jupyter notebooks to run analyses.

TIaaS URL for this training: https://usegalaxy.eu/join-training/gcc-intermine

avatar for Yo Yehudi

Yo Yehudi

Software Developer, University of Cambridge & Open Life Science
Integrated genomic data (InterMine)

Thursday July 4, 2019 15:50 - 17:20 CEST