Genetics InterMine API Training 2019-06-19

Schedule

• 13:30 Introduction - 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 20 June 2019) - “none” is an acceptable answer!
    • Poll results
• 14:00 🐍 Hands-on code along in Python (PAX6 Workflow):
  • Python Pax6 Workflow (unsolved):
  • Python Pax6 Workflow (with answers):
• 15:00 🇷 Advanced exercises: producing figures and data visualisations
  • Enrichment and visualisations (unsolved):
  • Enrichment and visualisations (with answers):
• 15:45 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)
  • 🇷 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.

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.