HBP Summit Satellite Events - Agenda(hide abstracts)
|Monday, 27 March 2023|
|09:00||HBP Summit Satellite Events|
The satellite event day can be visited free of charge, but a registration is needed (Registrations after 20 March will have name tags produced on-site):
The registration desk is situated at the main entrance of Palais du Pharo, 58, Boulevard Charles Livon, 13007 Marseille, France. Name tags can be picked up from 8:00 on Monday 27 March. Please note that only registered attendees will be able to access the venue on 27 March.
Some sessions may have links, software you should pre-install, or other requirements. Information is centrally available on the public wiki page here, please check it out before the event.
|1st parallel session|
License to Spike - A NEST Desktop and NESTML Workshop
In this session we give a tutorial of these tools which are parts of the ecosystem of NEST Simulator, an establisted tool for spiking neuronal networks. First, we show the frontend NEST Desktop which allows users to construct networks and explore activity without needs of programming. Next, we introduce NESTML which expresses neuron and synapse models which can be easily translated into simulation code. More information
Simulating complex neurobiological phenomena of human brain function and dysfunction in a data protection compliant environment: EBRAINS Service for Sensitive Data.
Simulating complex neurobiological phenomena of human brain function and dysfunction in a data protection compliant environment. A hands-on training offer for using EBRAINS Service for Sensitive Data to discover, access and use health data for personalized human brain simulations. More information
NMC (neuromorphic computing): hands on BrainScaleS
A hands-on tutorial for the first steps for online interactive use of the BrainScaleS neuromorphic compute system: from the first log-in via the Collaboratory to interactive emulation of small spiking neural networks. This hands-on tutorial is especially suitable for beginners (more advanced attendants are welcome as well). We are going to use the BrainScaleS tutorial notebooks for this event.
Vast parameter space exploration using L2L on EBRAINS
This workshop features a session on a hyper-parameter optimization framework implementing the concept of Learning to Learn (L2L). This framework provides a selection of different optimization algorithms and makes use of multiple high-performance computing back-ends (multi nodes, GPUs) to do vast parameter space explorations in an automated and parallel fashion (Yegenoglu et al. 2022). During this session, you will learn about the installation and use of this framework within EBRAINS. A TVB (Sanz Leon et al. 2013) simulation used in a study for a scale-integrated understanding of conscious and unconscious brain states and their mechanisms (Goldman et al. 2021) will serve as an example. In this study a set of 5 model variables has been explored, to find optimal parametrization for synchronous and a-synchronous brain states. Participants will learn how to launch a TVB simulation on Fenix’s high performing compute GPU backends using Unicore. Please create an JuDoor account and register to this project here
The process of integrating your science in an integrated EBRAINS workflow
This session demonstrates the work of the EBRAINS Science Liaison Unit (SLU) which facilitates the translation of science needs into technical requirements towards integration into EBRAINS. SLU provides several tools and processes designed to help you, in a hands-on co-design process, identify your needs and formulate from these a concrete description that will assist you in; homogenizing your data, getting in contact with potential collaborators, utilizing EBRAINS information sources, and find solutions both technical and scientific in nature. In addition, the computational requirements of your project can be used as input for the developers in the EBRAINS platform to build new or adapt existing functionality to help make your science wish and want a reality.
In this event, we will show you how our structured formalization process generates a detailed co-design document describing a full workflow that is capable of running on EBRAINS. The document includes a roadmap that consists of all the necessary descriptions to assess the needs of the research and how to achieve its objectives in a Fair science scenario ensuring reproducibility, availability, and visibility of the work.
Software delivery for the Lab and integration into the EBRAINS software release
A hands-on training session with a step-by-step demonstration of the procedure to build and deliver EBRAINS tools for the Lab: creation of Spack package, contribution to the EBRAINS official software release repository, automated test builds on gitlab runners, CI/CD workflow, validation in the lab-int and deployment to production. The session will also include a high-level overview of the build and delivery strategy: automated testing and deployment operations, official and experimental release schedule, steps and requirements for integration into the EBRAINS software release.
|2nd parallel session|
Publishing your research data through EBRAINS.eu
Making your research data discoverable and citable is key for attracting attention to your research and helping you meet the requirements from funders and journals. The EBRAINS Curation Team will show you how to get started with FAIR data sharing.
EBRAINS Medical Data Analytics
The EBRAINS Medical Data Analytics Service: share and re-use health data to accelerate progress in clinical neurosciences. Two unique platforms cover key areas in clinical research: The Medical Informatics Platform – MIP: privacy-preserving, federated data processing and analytics system for the federation of anonymized large clinical datasets and research cohorts. The Human Intracerebral EEG Platform -HIP: privacy-enabling environment for state-of-the-art processing and international sharing of human intracerebral EEG (iEEG) data. The MIP is a privacy-preserving, federated data processing and analytics system, working on decentralised patient data and research cohort datasets. It provides integrated statistical methods, predictive machine learning algorithms for data exploration, modelling, integration and data analysis methods. The HIP offers a data privacy-enabling environment for state-of-the-art processing and international sharing of human iEEG data. It offers a state-of-the art software library for data processing and analysis, and will provide unprecedented access to Human iEEG data for the world scientific community.
In this session you will see demos of the two platforms, hear about federation of decentralized medical data, learn about opportunities on how to use the MIP for your own applications and get an introduction and demos of the latest developments of the HIP, a brandnew platform for processing iEEG data.
|3rd parallel session|
Fenix User Forum meeting - How to make use of the Fenix Infrastructure
The Fenix User Forum, launched in January 2020, aims at facilitating the interaction between users and Fenix experts, as well as among users. The Forum offers Fenix users the opportunity to discuss and share their experiences, to express their needs, and to provide feedback on the current services and resources of the Fenix Infrastructure. Having launched the Forum at the HBP Summit 2020, we continued the tradition of Forum meetings at the HBP Summit 2021 and aim to do so at the HBP Summit 2023. The session will include presentations and demons on the currently available e-infrastructure services (provided by ICEI and HBP SGA3 WP6), examples of projects using Fenix resources, and details on how to access HPC, Cloud and storage resources of the Fenix Infrastructure. A major part of the session will be dedicated to an open discussion where current HBP/EBRAINS users and others interested in the Fenix Infrastructure can ask questions to the Fenix experts and provide feedback on how the provided Fenix services meet current user requirements and on prospective future requirements. Find the agenda page to this meeting here
Rodent atlasing tools and QUINT workflow
Workflows for image registration to an atlas and atlas based quantifications of cells or features in the experimental murine brain section images.
EBRAINS Documentation and Tutorial Hands-On Workshop
In this session, we will provide an overview of guidelines and helpful points for successful documentation creation in EBRAINS, including tips on writing, integrating and maintaining your docs. In the hands-on session, you will be able to develop your tutorial or other documentation material with direct feedback and have an opportunity to discuss issues, ensuring that your users have the information they need to use your tool or service.
WE ARE SCIENCE. Towards a realistic future to enhance inclusion, gender, equality, and diversity in science.
For this satellite event there is a separate agenda and registration page (free of charge as well). No EBRAINS account is needed for this satellite event.
|16:30||End of the HBP summit 2023 satellite events day|
|4th parallel session|
Standardised Workflows in EBRAINS
A hands-on training offer for Standardised Workflows in EBRAINS. A short presentation will be used as an introduction, while the main hands-on session will provide information about Writing and Executing Standardised Workflows. TC will give some guidelines, so attendees can experiment with writing CWL tools and workflows and then they will be given access to VM to execute these workflows. The Workflows Dashboard will be also presented during the same session, offering to the attendees the opportunity to understand the different functionalities, use it with TC support and provide useful comments.
Arbor: the future of simulation. User reports, benchmarks, an interactive session, and discussion of your simulation needs.
The session will introduce Arbor, the only morphologically detailed simulator developed entirely under the auspices of the HBP as a cooperation between primarily FZJ and CSCS, and with significant contributions from Pavia, Erasmus, Heidelberg, Barcelona, Goettingen, Oslo, through connections established with an HBP CEoI. Showcased will be the Arbor, the Arbor GUI, and a selection of research that has been done with Arbor so far. Depending on audience and time (we are still preparing contributions to the showcase), we would allocate time to give attendees a hands-on on their own machines and/or the EBRAINS Lab.
Reconstructing and simulating multiscale brain circuits: workflows and applications to function and dysfunction
A theoretical introduction and hands-on training using EBRAINS to reconstruct and simulate brain microcircuits and embed them into virtual brain models for integrated co-simulations.