Handling integrated biological data using Python, Jupyter, and InterMine

Galaxy Community Conference July 4 2019

Short link to this page: bit.ly/intermine-gcc2019

Schedule and materials

• 15:50 Introduction: What is InterMine? Intro to the User Interface. Slides
• 16:10 APIs: What is an API and why might we use one?
  • API slides
  • Poll: What programming language(s) do you use as part of work, if any?
    • Please take 20 seconds to vote in this poll (closes 05 July 2019) - “none” is an acceptable answer!
    • Poll results
• 16:20 🐍 Hands-on code along in Python (PAX6 Workflow):
  • Python Pax6 Workflow (unsolved):
  • Python Pax6 Workflow (with answers):
• Self-learn exercises - use cases and questions. Your choice of:
  • 🐍 Python: API Exercises
  • 🇷 R Pax6 Workflow (same results as the Python workflow, but in R)
    • R Pax6 Workflow (unsolved)
    • R Pax6 Workflow (with answers)
  • 🇷 Advanced exercises: producing figures and data visualisations
    • Enrichment and visualisations (unsolved):
    • Enrichment and visualisations (with answers):
  • 🐍 or 🇷: Replicate some of the exercises we’ve run today on your favourite organism or favourite genes / proteins. We can help walk you through it and troubleshoot where needed.
• 17:10 Moving data between Galaxy and InterMine

Useful links

🐍 Python

• Python tutorial
• Python API docs

🇷 R

• InterMineR on Bioconductor - includes links to the reference manual, vignettes, and install instructions.

Which InterMine is for me?

• InterMine Registry - search for your favourite organism(s). There are tens of InterMines and some InterMines cover a large number of organisms.

Support:

• There are lots of links on intermine.org - in particular see the developers section for documentation and the contact section for support.