Simulate with EBRAINS

How to use EBRAINS research infrastructure and Fenix resources for simulations on a scale from molecules via small and large networks of point or structured spiking neurons to simplified whole brain activity and virtual environments.

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Talk recordings

Many talks of the event will be available as recordings.

• Some of the recordings are accessible publicly without account or login and are linked directly in the agenda below.
• Some talks are accessible only for people, who were registered attendants to the meeting and are linked on their personal meeting page.

Abstract

This online workshop aims at giving an overview of how to simulate with EBRAINS, from the infrastructure level to simulations at multiple scales. It covers a large variety of topics, e.g. computing and data services of or related to the Fenix infrastructure, Neuromorphic Computing, and simulations on a scale from molecules via small and large networks of point or structured spiking neurons to simplified whole brain activity and virtual environments Participants can choose from a large number of sessions what is relevant for them. The first day will be a short workshop about the Fenix User and Resource Management Service (FURMS) and the Fenix Authentication & Authorisation Infrastructure (AAI). The second day will start with the official welcome session, followed by introductions to the different topics of this workshop and to put tools and simulators into relation with each other. These introductions also serve the purpose to help the participants to update their choice of sessions for the following days. This day will conclude with a hands-on introduction to the EBRAINS Collaboratory environment, a web-portal through which many services and tool are available, and which will be used by several sessions on the following days. The last two days are organised with multiple sessions taking place in parallel, in which the tools and services will be presented in more detail, with lectures and/or as hands-on tutorials.

Registration to the event was free of charge, but registration was necessary.

Venue: Online

The training event took place as an online zoom video conference.

Agenda structure:

• 7 November: Fenix User and Resource Management Service (FURMS) and Fenix AAI (level: for specialists)
• 8 November: introductions to the tools and a hands-on introduction to the EBRAINS Collaboratory environment (level: suitable for first time EBRAINS users)
• 9&10 November: parallel tracks showing different tools available in the EBRAINS research infrastructure, some of them as hands-on tutorials

This workshop will provide attendees with the latest updates about both the Fenix Authentication and Authorization Infrastructure (Fenix AAI) and Fenix User and Resource Management Service (FURMS). Together, Fenix AAI and FURMS enable a federated identity and access management service including accounting and reporting of resources across the Fenix sites. The workshop will provide an overview of the current status and developments of Fenix AAI and FURMS, and will present demos of how to use both services.

Material for some sessions is available here.

Please use this dial in link to access the zoom meeting.

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This day starts with brief introductions to the tools in the morning, followed by a tour from beginner to expert of the EBRAINS "Collaboratory". This is the interface for collaboratively working in teams with documents and accessing services (e.g. using Jupyter notebooks).

Please use this dial in link to access the zoom meeting (all parts of the agenda on 8 November are available via this dial-in).

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Suggestion: check out the Your contribution to shaping the course of neuroscience paper process.

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(Very) short introductions into all the tools and services (simulations tools, emulations, computing, analysis, ...) covered during this training workshop.

Please see the agenda below for the covered tools and some additional information on the respective session (please use the agenda in the view with all abstracts unfolded)

• Macromolecular flexibility databases; Setting up & running Molecular Dynamics (MD) simulations
• SSB toolkit: from molecular structure to subcellular networks
• τ-RAMD: Estimation of residence time and determination of unbinding pathways
• MiMiC: Mutiscale QM/MM simulations of ligand-enzyme complex with MiMiC

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• Electrical model building toolset
• NEURON / CoreNEURON: building and using computational models of neurons and networks of neurons
• Arbor: portable, high-performance library for computational neuroscience simulations

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• PyNN: Using the PyNN library to build and simulate spiking neural network models on EBRAINS
• NEST Desktop: web-based graphical user interface (GUI) for the NEST Simulator.
• NESTML: language for neuron and synapse models.

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• CINECA HPC
  • Scalable Compute on Galileo100 platform
  • HPC Cloud Computing infrastructure at CINECA
  • BURST buffering
• Central Data Transfer Services

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Links:

• OIDC Clients : https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation IAM/FAQ/OIDC Clients explained/How Bearer Access Token works/
• Search EBRAINS users: https://wiki.ebrains.eu/bin/view/Identity/#/users
• Browse units : https://wiki.ebrains.eu/bin/view/Identity/#/units/all
• Search Groups : https://wiki.ebrains.eu/bin/view/Identity/#/groups
• Demo collab link: https://wiki.ebrains.eu/bin/view/Collabs/demo-collab
• Documentation collab link: https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/
• Support link: https://ebrains.eu/support
• Registration link: https://ebrains.eu/register/

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Links:

• Lab link: https://lab.ebrains.eu/hub/login
• nbgitpuller: https://jupyterhub.github.io/nbgitpuller/link
• Chrome addon: https://github.com/yuvipanda/nbgitpuller-link-generator-webextension#on-google-chrome--chromium
• Firefox addon: https://addons.mozilla.org/en-US/firefox/addon/nbgitpuller-link-generator/

This will be an introduction to Jupyter Lab (=execution of python programs in the browser, no additional software installation on the client needed), and Python notebooks.

We will look at:

• a few examples of basic Python notebooks,
• a real notebook using EBRAINS tools,
• how the Lab can be used with notebooks in a git repository,

The session will include some time for hands-on for users to try out notebooks.

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This session is more specifically targeted at developers of EBRAINS services and tools.

Links:

• Documentation: https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation IAM/FAQ/OIDC Clients explained/1. Registering an OIDC client v2/
• Notebook to create and manage OIDC client: https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation IAM/FAQ/OIDC Clients explained/1. Registering an OIDC client v2/
• OIDC group requirement: https://wiki.ebrains.eu/bin/view/Identity/#/groups/app-collaboratory-iam--service-providers
• How to register an OIDC client: https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation IAM/FAQ/OIDC Clients explained/1. Registering an OIDC client v2/
• All OIDC endpoints: https://iam.ebrains.eu/auth/realms/hbp/.well-known/openid-configuration
• mozilla-django-OIDC documentation: https://mozilla-django-oidc.readthedocs.io/en/stable/installation.html
• Flask-OIDC: https://flask-oidc.readthedocs.io/en/latest/
• Mozilla-Django-OIDC-demo: https://github.com/HumanBrainProject/mozilla-django-oidc-demo
• Quota manager collab: https://wiki.ebrains.eu/bin/view/Collabs/quota-management
• Quota manager API: https://wiki.ebrains.eu/bin/view/Collabs/quota-management/API

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Please find the dial-in links for the sessions in the table headers below.

• NEST Desktop: a web-based graphical user interface (GUI) for the NEST Simulator
• TVB: demonstrating the TVB-EBRAINS integrated end-to-end personalized brain simulation workflows in the Cloud. For a more detailed agenda of this part see here on brainsimulation.org
• Electrical model building toolset: build a biologically detailed neuron model using the NEURON simulator and the open source python packages: eFEL, BluePyEfe and BluePyOpt.

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• NESTML: a domain-specific language for neuron and synapse models
• PyNN: Using the PyNN library to build and simulate spiking neural network models on EBRAINS

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• Neuron / CoreNEURON: An introduction of NEURON and how to run existing models with CoreNEURON
• Health Data Cloud: an introduction to EBRAINS Service for Sensitive Data - the Health Data Cloud (HDC). For a more detailed agenda of this part see here on brainsimulation.org
• Arbor: a portable, high-performance library for computational neuroscience simulations with multi-compartment, morphologically-detailed cells
• MUSIC: a tool for co-simulation in the computational neuroscience domain

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Please find the dial-in links for the sessions in the table headers below.

• Central Data Transfer Services: data transfer in Fenix (material)
• Macromolecular flexibility databases; Setting up & running Molecular Dynamics (MD) simulations
• The Neurorobotics Platform (NRP) is a set if software tools to enable its users to connect brain models to embodied agents interacting with a simulated environment.

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• HPC Cloud Computing infrastructure at CINECA; hands on configuring an using a virtual machine in the CINECA cloud infrastructure
  followed by
  brief overview of the framework that Cineca adopted as interactive computing interface
• MiMiC: Mutiscale QM/MM simulations of ligand-enzyme complex with MiMiC (instructions for accessing HPC resources, additional material)
• BrainScaleS: hands-on the physical emulation neuromorphic compute system BrainScaleS

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• BURST buffering: BURST buffering: how to benefit from a fast data tier
• Elephant: a data analysis frmework for electrophysiological activity data

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