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.

This session is of interest to the Developers/Component Owners(COs) who wish to have the software of their Component built and delivered centrally (EBRAINS integration) for the Collaboratory Lab. To enable the integration of software for the Collaboratory Lab environment all that is required by COs is to prepare a Spack package (python file) which details all build instructions that Spack needs to be aware of in order to successfully perform the build and install operations. In this session we will present the build and delivery strategy and explain how software can be built and delivered for the Lab environment from the creation of the Spack package, to transferring it over to the Technical Coordination pipeline and finally accessing the software on the Lab.

(no-slides demo of the live papers)

We are pleased to present a new service under EBRAINS called "Live Papers". EBRAINS Live Papers are interactive documents bringing together code, models, and data. It aims to enable researchers to easily access data resources employed in published studies and understand better the provenance of published results and figures. This significantly enhances the utility of scientific outputs, such as published models and datasets, and also supports the reproducibility of data analyses. Interactivity is a prominent feature with several integrated tools and services that allow users to download, visualise or simulate data, models and results presented in the corresponding publications. It allows for easily linking to resources in community databases such as EBRAINS, NeuroMorpho.org, ModelDB, the Allen Brain Atlas, thereby acting as an integrator of scientific resources spanning diverse data types such as models, morphologies, electrophysiological data and Jupyter notebooks. Issuance of a DOI further assists the citation of published data and models, thereby incentivising authors to publish and share such resources, and ensuring that they are duly acknowledged when these resources are reused. Community-based, collaborative modelling efforts can also greatly benefit from this platform.

Recent developments enhance features and interoperability of various EBRAINS infrastuctures. In this session we will have a look at what is currently already possible on a concrete example of playing with existing models in JupyterLab. The idea is to have an open and interactive discussion to bring perspectives of the audience together and work towards sustainable concepts of using the EBRAINS infrastructures. We will touch on topics like the development and maintainability of Jupyter notebooks, testing and validation, the link to HPC/NM backends, and automated workflows. Bringing the different available tools and features together in a user-understandable yet sustainable and maintainable way is key for EBRAINS to be more than the sum of its parts and prevail in the light of constant changes of infrastructure and research in the years to come.

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.