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ELIXIR | Biological Data Analysis Using InterMine

Date:

Thursday, 3rd September

Time:

17:00 to 20:00 (CEST)

Organisers

  • Rachel Lyne | University of Cambridge, United Kingdom
  • Daniela Butano | University of Cambridge, United Kingdom

Summary

InterMine is a well-established open-source data warehouse built specifically for the integration and analysis of complex biological data.  Many groups use the InterMine framework to provide a query and analysis platform for their data and there is now a broad selection of InterMine databases worldwide, covering many organisms, including HumanMine, PhytoMine (over 87 plant genomes), Hymenoptera, Planaria, the Legume federation InterMines (Chickpea, Soy, Legume, Peanut, Bean), MedicMine (Medicago), ThaleMine (Arabidopsis) as well as the budding yeast, rat, zebrafish, mouse, fly and nematode model organisms. 

The InterMine framework includes a user-friendly web interface as well as a powerful web service API, with multiple language bindings including Python and R.   This workshop will introduce both aspects of InterMine, first covering querying data through the user interface and then looking at how similar analysis can be carried out using the API, with examples in Python.

Target audience

The workshop is suitable for researchers from a broad biological background as the techniques learned can be applied to any InterMine database, covering a diverse range of organisms and biological data.  No previous experience of InterMine or Python is required.  The automatic code generation feature of InterMine means that the programming side is accessible to beginners. However, researchers with programming experience would also benefit from this tutorial, learning how the InterMine API can be applied to the biological techniques taught.

Schedule

Time
Details
17:00 - 17:30 Welcome and Introduction to querying omics data with InterMine
17:30 - 18:30 Practical Demo: Using the InterMine user Interface.  Short demonstrations and practical exercises.
18:30 - 18:45 Break
18:45 - 19:00 Web Service API Introduction:  What is an API and basic examples of accessing them
19:00 - 20:00 Using the InterMine API:  automatic code generation and an in-depth walkthrough of the code to create the same analyses shown in the web interface section. We will use Python for the examples.