CodeJam #12 - Agenda

The 12th CodeJam will focus on EBRAINS infrastructure themes.

The CodeJam follows the successful model from the previous CodeJams: mainly interactive working sessions of developers and a few talks about general interest topics from the EBRAINS overall computing / service system.

The registration for the CodeJam is free of charge.

Dial-in

The dial-in information for the meeting is provided for the registered attendants on their individual personal page for the meeting.

Restricted access material

• Some talk videos and presentations may only be available on the personal page (for registered meeting attendants only).
• If you did not log in with your EBRAINS account yet: some additional material may be accessible on the logged in version of this agenda.

(no slides - showed things live)

(no-slides talk)

(no-slides talk)

(no-slides talk)

Work together with your collaborators in breakout rooms on your projects.

• Project 1: Mini-hackathon on fairgraph and the openMINDS Python API - Andrew Davison (cnrs) and Stefan Köhnen (jülich) - (Breakout room "Project 1)
• Project 2: Extending ebrains-drive Python client - Shailesh Appukuttan (cnrs)

Work together with your collaborators in breakout rooms on your projects.

show abstract

(no-slides demo of the live papers)

show abstract

show abstract

Before starting to the Coffee break, we would like to invite you to a "group photo" (= screen shots of the zoom gallery view). We want to use the group photo for HBP / EBRAINS dissemination and outreach = it will show up on the web, on twitter, ....

Please thus ONLY turn your camera on, if you are OK with that use (we will blank out the names, only the image will be in the released picture).

This session is of interest to Scientists and Developers of the Consortium who wish to have a more in-depth understanding of Standardized Computational Workflows.

Format of the session will be as follows:

• A presentation of our work introducing the benefits of defining workflows in a standard format, as well as the technologies technical coordination team is proposing. More specifically, defining workflows and command line tools in a common standard and widely accepted way using Common Workflow Language will be introduced. Wrapping command line tools that are used in workflow steps via containerization methods (Docker) will also be presented as well as Long term / Short term vision of our work.
• A hands–on session on the proposed technologies (CWL, Docker) will be held. In this section we will provide detailed information with concrete examples on how we define workflows and command line tools via Common Workflow Language and how we wrap tools via Docker containerization methods with all the libraries, binaries needed. We will also dive in the execution part of standardized workflows on different underlying infrastructures (locally, VMs, HPC systems).

You can already take a look under the documents already shared with the Consortium:

• Standardized Computational workflows at EBRAINS dedicated –but not limited- to scientists
• Hands-on standardized computational workflows dedicated – but not limited – to developers.
• EBRAINS GitLab repo with our work

If you find this interesting, bring your work and come along asap for Accessible, Scalable, Automated, Portable (ASAP) workflows!

Work together with your collaborators in breakout rooms on your projects.

In parallel in breakout rooms -- not recorded:

• Project 4: Further discussion on “Low threshold research” - Dennis Terhorst (Zoom breakout room "Project 4")
• Project 5: Discuss new features to enhance functionality of Live Papers - Shailesh Appukuttan (Zoom breakout room "Project 5")

Work together with your collaborators in breakout rooms on your projects.

• CET 10:00h Project 6: PyNN related discussion in "PyNN related"

We will present technical and organizational measures that we employed to create a GDPR compliant Virtual Research Environment (VRE) for complex simulations and analytics of sensitive health data. The VRE forms the basis for the EBRAINS Health Data Cloud that provides coordinated governance and GDPR compliance, a federated ecosystem including code to data solutions, interoperability with a centralized Knowledge Graph for discoverability, access control, encryption, sandboxing and cross-site identity management, collaboration resources and an API gateway for seamless interaction between participating nodes/IT centers.

Talk cancelled.

Work together with your collaborators in breakout rooms on your projects.

Breakout rooms 1-15 are open through the day.

Special groups:

• CET 17:15h: BrainScaleS-2 demo: in the main zoom session
• CET 17:15h: Project 4: Further discussion on “Low threshold research” - Dennis Terhorst in "Room 2"

Project 8: Programmatic workflows with EBRAINS brain atlases using siibra-python - (Zoom breakout room "Project 7) - 60min.