Tools for OME Training and Outreach

OME Users meeting
30th May 2018
Jean-Marie Burel

Outline

• Growing ecosystem
• Aims
• Joining the pieces...
• What's available
• Is it worth it?

Training ecosystem before...

Training ecosystem now

First Aim

• Provide training materials that join pieces of the ecosystem together

Joining the pieces...

Workflows & Permissions

More Aims

• Provide reusable training materials
• Provide resources for setting up training sessions
• Have resources publicly available
• Have resources under Version Control

What's available

New repositories: ome/training-*

• Overarching repository: ome/training-repos

  • openmicroscopy/prod-playbooks Ansible playbook to deploy a training server
  • ome/training-scripts: Training server maintenance/data preparation
  • ome/training-scripts: Training scripts e.g. Python, Java, Jython, etc.
  • Data used for a given session
  • presentations used for a given session

Resources

• Data:

  • https://downloads.openmicroscopy.org/images/
  • IDR: https://idr.openmicroscopy.org/
  • Other e.g. https://doi.org/10.5281/zenodo.16956

• Presentations/Printout:

  • https://downloads.openmicroscopy.org/presentations
  • https://github.com/ome/presentations

Dedicated servers

• OMERO: https://demo.openmicroscopy.org/
  • Sign up for an account
• IDR (Read-only): https://idr.openmicroscopy.org/
  • Public access

Analysis environment

Sets of Notebooks

• For OMERO training
• For IDR training

Is it worth it?

Day 2 Metadata workshop

• Server:outreach.openmicroscopy.org
  • users have access after session for 1 week when possible
• Data Source: IDR
• Users-Meeting/Workshops: :Presentations/Printout
• Metadata workshops workflow

Thank you