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CodeJam #12 - Agenda
(show all abstracts)| Tuesday, 23 November 2021 | |||
| HBP / EBRAINS: CodeJam #12: EBRAINS interactive usage and mutli-site worfklows 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-inThe dial-in information for the meeting is provided for the registered attendants on their individual personal page for the meeting. Restricted access material
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| CET: 13:00 UTC: 12:00 | Opening Session | ||
| CET: 13:00‑13:05 UTC: 12:00‑12:05 (5 min) | Short welcome and technical note from the Programme Committee | Andrew Davison (cnrs) | |
| CET: 13:05‑13:15 UTC: 12:05‑12:15 (10+5 min) | Introduction to EBRAINS RI show presentation.pdf (public accessible) show talk video | Amaryllis Raouzaiou (athena) | |
| CET: 13:20 UTC: 12:20 | Session 1 - Accessing and analysing data in EBRAINS | ||
| CET: 13:20‑13:30 UTC: 12:20‑12:30 (10+5 min) | Drive API / Python client show presentation.pdf (public accessible) (a video of this talk is available for EBRAINS account owners: show video) | Shailesh Appukuttan (cnrs) | |
| CET: 13:35‑13:45 UTC: 12:35‑12:45 (10+5 min) | Collaboratory Buckets, UI and programmatic access show talk video (no slides - showed things live) | Alexis Durieux (ebrains) | |
| CET: 13:50‑14:00 UTC: 12:50‑13:00 (10+5 min) | Large data transfers between ICEI sites show presentation.pdf (only with login + special group membership) | Sandra Diaz (juelich) | |
| CET: 14:05‑14:15 UTC: 13:05‑13:15 (10+5 min) | Data analysis with Elephant (the presentation .pdf is accessible for meeting attendants from their 'personal page') (a video of this talk is available for meeting attendants. Please check your personal meeting page (for EBRAINS account owners: personal meeting page and show video)) | Michael Denker (juelich) | |
| CET: 14:20‑14:30 UTC: 13:20‑13:30 (10+5 min) | Siibra-python / Siibra API (no-slides talk) | Timo Dickscheid (juelich) | |
| CET: 14:35‑14:45 UTC: 13:35‑13:45 (10+5 min) | Frites show presentation.pdf (public accessible) show talk video | Andrea Brovelli (amu) | |
| CET: 14:50 UTC: 13:50 | Session 2 - Programmatic access to the KG | ||
| CET: 14:50‑15:00 UTC: 13:50‑14:00 (10+5 min) | General overview to openMINDS show presentation.pdf (public accessible) show talk video | Lyuba Zehl (juelich) | |
| CET: 15:05‑15:15 UTC: 14:05‑14:15 (10+5 min) | openMINDS Python API show presentation.pdf (public accessible) show talk video | Stefan Köhnen (juelich) | |
| CET: 15:20‑15:30 UTC: 14:20‑14:30 (10+5 min) | KG Query API and Builder (no-slides talk) | Oliver Schmid (ebrains) | |
| CET: 15:35‑15:45 UTC: 14:35‑14:45 (10+5 min) | Fairgraph show presentation.pdf (public accessible) show talk video | Andrew Davison (cnrs) | |
| CET: 15:50‑16:20 UTC: 14:50‑15:20 (30 min) | Coffee Break | ||
| CET: 16:20 UTC: 15:20 | Session 3 - Simulation Tools I | ||
| CET: 16:20‑16:30 UTC: 15:20‑15:30 (10+5 min) | News on NEST show presentation.pdf (only with login + special group membership) (a video of this talk is available for meeting attendants. Please check your personal meeting page (for EBRAINS account owners: personal meeting page and show video)) | Dennis Terhorst (juelich) | |
| CET: 16:35‑16:45 UTC: 15:35‑15:45 (10+5 min) | NESTML show presentation.pdf (public accessible) (a video of this talk is available for EBRAINS account owners: show video) | Charl Linssen (juelich) | |
| CET: 16:50‑17:00 UTC: 15:50‑16:00 (10+5 min) | Arbor show presentation.pdf (public accessible) show talk video | Brent Huisman (juelich) | |
| CET: 17:05‑17:15 UTC: 16:05‑16:15 (10+5 min) | Cellular simulation services show talk video (no-slides talk) | Stefano Antonel (epfl) | |
| CET: 17:20‑17:30 UTC: 16:20‑16:30 (10+5 min) | Brain Scaffold Builder (BSB) design and use cases show presentation.pdf (public accessible) show talk video | claudia casellato (unipv) | |
| CET: 17:35 UTC: 16:35 | Project Work Work together with your collaborators in breakout rooms on your projects. | ||
| CET: 17:35‑17:50 UTC: 16:35‑16:50 (15+5 min) | Kick-off: proposals for break-out sessions for the week | all | |
| CET: 17:55‑18:30 UTC: 16:55‑17:30 (35 min) |
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| CET: 18:30 UTC: 17:30 | End of Day 1 (project work can go on) | ||
| Wednesday, 24 November 2021 | |||
| CET: 09:00 UTC: 08:00 | CodeJam#12, day II | ||
| CET: 09:00‑12:00 UTC: 08:00‑11:00 (180 min) | Project Work Work together with your collaborators in breakout rooms on your projects. | all | |
| CET: 12:00‑13:00 UTC: 11:00‑12:00 (60 min) | Lunch Break | ||
| CET: 13:00 UTC: 12:00 | Session 4 – Building EBRAINS | ||
| CET: 13:00‑13:40 UTC: 12:00‑12:40 (40+5 min) | Software Delivery and Installation for the Lab show presentation.pdf (public accessible) show talk video | Athanasios Karmas (athena) | |
| CET: 13:45‑13:55 UTC: 12:45‑12:55 (10+5 min) | Creating an OIDC client and using it from Python | Axel Messinese (ebrains) | |
| CET: 14:00‑14:10 UTC: 13:00‑13:10 (10+5 min) | Deploying a Javascript browser-side Community app | François Bougault (ebrains) | |
| CET: 14:15‑14:25 UTC: 13:15‑13:25 (10+5 min) | EBRAINS Live Papers (a video of this talk is available for EBRAINS account owners: show video) (no-slides demo of the live papers) | Shailesh Appukuttan (cnrs) | |
| CET: 14:30‑14:55 UTC: 13:30‑13:55 (25+5 min) | Low threshold research 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. | Dennis Terhorst (juelich) | |
| CET: 15:00‑15:05 UTC: 14:00‑14:05 (5 min) | Group photo 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).
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| CET: 15:05‑15:30 UTC: 14:05‑14:30 (25 min) | Coffee Break | ||
| CET: 15:30 UTC: 14:30 | Session 5 – Workflows | ||
| CET: 15:30‑15:55 UTC: 14:30‑14:55 (25+5 min) | Role of the SLU / State of the Showcases show presentation.pdf (public accessible) (a video of this talk is available for meeting attendants. Please check your personal meeting page (for EBRAINS account owners: personal meeting page and show video)) | Wouter Klijn (juelich) | |
| CET: 16:00‑16:40 UTC: 15:00‑15:40 (40+5 min) | Standardized computational workflows show presentation.pdf (public accessible) video (restricted access) 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. | sofia karvounari (athena) | |
| CET: 16:45‑16:55 UTC: 15:45‑15:55 (10+5 min) | Provenance API show presentation.pdf (public accessible) (a video of this talk is available for EBRAINS account owners: show video) | Andrew Davison (cnrs) | |
| CET: 17:00 UTC: 16:00 | Project Work Work together with your collaborators in breakout rooms on your projects. | ||
| CET: 17:00‑18:30 UTC: 16:00‑17:30 (90 min) | Project 3: Demo / Tutorial / Hands-on session with CWL workflows (main room) video (restricted access) In parallel in breakout rooms -- not recorded:
| Eleni Mathioulaki (athena) | |
| CET: 18:30 UTC: 17:30 | End of Day 2 (project work can go on) | ||
| Thursday, 25 November 2021 | |||
| CET: 09:00 UTC: 08:00 | CodeJam#12, day III | ||
| CET: 09:00‑12:00 UTC: 08:00‑11:00 (180 min) | Project Work Work together with your collaborators in breakout rooms on your projects.
| all | |
| CET: 12:00‑13:00 UTC: 11:00‑12:00 (60 min) | Lunch Break | ||
| CET: 13:00 UTC: 12:00 | Session 6 – EBRAINS Health Data Cloud 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. | ||
| CET: 13:00‑13:25 UTC: 12:00‑12:25 (25+5 min) | Technical and organizational measures for GDPR compliant Virtual Research Environments (VRE)(the presentation .pdf is accessible for meeting attendants from their 'personal page') show talk video | Petra Ritter (charite) | |
| CET: 13:30‑13:55 UTC: 12:30‑12:55 (25+5 min) | Demo: GDPR compliant TVB image processing container workflows with HPC on EBRAINS show presentation.pdf (public accessible) show talk video | Michael Schirner (charite) | |
| CET: 14:00‑14:25 UTC: 13:00‑13:25 (25+5 min) | Demo: TVB GDPR compliant simulation workflows with HPC on EBRAINS show presentation.pdf (public accessible) show talk video | Paula Popa (codemart) | |
| CET: 14:30‑14:55 UTC: 13:30‑13:55 (25+5 min) | Demo TVB-Cloud complex workflows in a GDPR compliant Virtual Research Environment(the presentation .pdf is accessible for meeting attendants from their 'personal page') show talk video | Moyez Dharsee, Fan Dong, and Susan Evans (indocresearch) Patrik Bey (charite) | |
| CET: 15:00‑15:30 UTC: 14:00‑14:30 (30 min) | Coffee Break | ||
| CET: 15:30 UTC: 14:30 | Session 7 - Simulation Tools II | ||
| CET: 15:30‑15:40 UTC: 14:30‑14:40 (10+5 min) | SpiNNaker show presentation.pdf (public accessible) show talk video | Andrew Rowley (uman) | |
| CET: 15:45‑15:55 UTC: 14:45‑14:55 (10+5 min) | LFPy show presentation.pdf (public accessible) (a video of this talk is available for meeting attendants. Please check your personal meeting page (for EBRAINS account owners: personal meeting page and show video)) | Espen Hagen (nmbu) | |
| CET: 16:00‑16:10 UTC: 15:00‑15:10 (10+5 min) | Electrical model building toolset show presentation.pdf (only with login + special group membership) (a video of this talk is available for EBRAINS account owners: show video) | Tanguy Damart (epfl) | |
| CET: 16:15‑16:25 UTC: 15:15‑15:25 (10+5 min) | BrainScales integration: Initiate your emulations via the Collaboratory show presentation.pdf (only with login + special group membership) show talk video | Eric Müller (uhei) | |
| CET: 16:30‑16:40 UTC: 15:30‑15:40 (10+5 min) | Navigation neural model implemented in the NRP show presentation.pdf (public accessible) show talk video | Simone Coppolino (cnr) | |
| CET: 16:45‑16:55 UTC: 15:45‑15:55 (10+5 min) | Neurorobotics platform show presentation.pdf (public accessible) | Fabrice Morin (tum) | |
| CET: 17:00‑17:10 UTC: 16:00‑16:10 (10+4 min) | Building NEURON microcircuits using touch detection with Snudda show presentation.pdf (public accessible) show talk video | Johannes Hjorth (kth) | |
| CET: 17:14 UTC: 16:14 | Talk cancelled. | Mikael Djurfeldt (kth) | |
| CET: 17:15 UTC: 16:15 | Project Work Work together with your collaborators in breakout rooms on your projects. Breakout rooms 1-15 are open through the day. Special groups:
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| CET: 17:15‑18:45 UTC: 16:15‑17:45 (90 min) | Project 7: BrainScaleS-2 interactive demo (20 min.) - (In the main zoom session) (a video of this talk is available for meeting attendants. Please check your personal meeting page (for EBRAINS account owners: personal meeting page and show video)) | Jakob Kaiser (uhei) | |
| CET: 18:45 UTC: 17:45 | End of Day 3 (project work can go on) | ||
| Friday, 26 November 2021 | |||
| CET: 09:00 UTC: 08:00 | CodeJam#12, day IV | ||
| CET: 09:00 UTC: 08:00 | Session 8 - BIDS computational modelling | ||
| CET: 09:00‑09:05 UTC: 08:00‑08:05 (5+5 min) | Introduction(the presentation .pdf is accessible for meeting attendants from their 'personal page') show talk video | Petra Ritter (charite) | |
| CET: 09:10‑09:25 UTC: 08:10‑08:25 (15+5 min) | BIDS extension proposal comp modeling show presentation.pdf (public accessible) show talk video | Michael Schirner (charite) | |
| CET: 09:30‑09:45 UTC: 08:30‑08:45 (15+5 min) | Demo of example data in BIDS comp modeling format(the presentation .pdf is accessible for meeting attendants from their 'personal page') | Jil Meier (charite) | |
| CET: 09:50‑11:50 UTC: 08:50‑10:50 (120 min) | Project Work Project 8: Programmatic workflows with EBRAINS brain atlases using siibra-python - (Zoom breakout room "Project 7) - 60min. | Xiao Gui (juelich) | |
| CET: 12:00 UTC: 11:00 | End of the CodeJam#12 | ||
