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Simulate with EBRAINS - Agenda

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Monday, 7 November 2022
CET: 09:00
UTC: 08:00

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
CET: 09:00
UTC: 08:00
First day: FURMS & Fenix AAI

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.

CET: 09:00‑09:15
UTC: 08:00‑08:15
(15 min)
 Welcome

.ics

Alex Upton (CSCS Swiss National Supercomputing Centre)
CET: 09:15‑09:30
UTC: 08:15‑08:30
(15 min)
 Introduction round of attendees (interest/involvement in Fenix AAI & FURMS)

.ics

Alex Upton (CSCS Swiss National Supercomputing Centre)
CET: 09:30‑10:15
UTC: 08:30‑09:15
(45 min)
 Introduction and latest developments in Fenix AAI

.ics

Michele Carpene (Italian National Supercomputing Consortium)
CET: 10:15‑10:30
UTC: 09:15‑09:30
(15 min)
 Demo of accessing different ICEI-Fenix OpenStack systems using Fenix AAI with EBRAINS account

.ics

Alex Upton (CSCS Swiss National Supercomputing Centre)
CET: 10:30‑10:35
UTC: 09:30‑09:35
(5 min)
 Open discussion about Fenix AAI

.ics

(all)
CET: 10:35‑11:20
UTC: 09:35‑10:20
(45 min)
 Introduction and latest developments in FURMS

.ics

Björn Hagemeier (Forschungszentrum Juelich GmbH)
CET: 11:20‑11:35
UTC: 10:20‑10:35
(15 min)
 FURMS Site perspective: demo of FURMS in production at BSC

.ics

Sergi More (Barcelona Supercomputing Center)
CET: 11:35‑11:40
UTC: 10:35‑10:40
(5 min)
 Open discussion about FURMS

.ics

(all)
CET: 11:40‑11:55
UTC: 10:40‑10:55
(15 min)
 Summary of workshop and closing remarks

.ics

Alex Upton (CSCS Swiss National Supercomputing Centre)

Tuesday, 8 November 2022
CET: 09:00
UTC: 08:00
Simulate with EBRAINS: Introductions and the EBRAINS Collabortory

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).

CET: 09:00‑09:05
UTC: 08:00‑08:05
(5 min)
Welcome

.ics

CET: 09:05‑09:25
UTC: 08:05‑08:25
(20+5 min)
EBRAINS for YOUR research show presentation.pdf (public accessible)

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

.ics

Katrin Amunts (Forschungszentrum Juelich GmbH)
CET: 09:30
UTC: 08:30
Introductions to all the tools covered in this training

(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)

CET: 09:30
UTC: 08:30
Introductions: molecular & sub-celluar simulators
CET: 09:30‑09:40
UTC: 08:30‑08:40
(10+5 min)
 Introductions to tools:
  • 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

.ics

Susanne Kunkel (Norwegian University of Life Sciences (NMBU))
CET: 09:55
UTC: 08:55
Introductions: cellular & network level software simulators
CET: 09:55‑10:05
UTC: 08:55‑09:05
(10+5 min)
 Overview about cellular level software simulators
  • 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

.ics

Susanne Kunkel (Norwegian University of Life Sciences (NMBU))
CET: 10:10‑10:20
UTC: 09:10‑09:20
(10+5 min)
 Overview about network level software simulators
  • 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.

.ics

Susanne Kunkel (Norwegian University of Life Sciences (NMBU))
CET: 10:25
UTC: 09:25
Introduction: whole brain level simulation
CET: 10:25‑10:30
UTC: 09:25‑09:30
(5+1 min)
 TVB (The Virtual Brain)

.ics

Petra Ritter
CET: 10:31
UTC: 09:31
Introductions: Neuromorphic Computing and Neurorobotics
CET: 10:31‑10:36
UTC: 09:31‑09:36
(5+1 min)
 Neuromorphic computing with SpiNNaker: real-time large spiking neural network simulations

.ics

Andrew Rowley (The University of Manchester)
CET: 10:37‑10:42
UTC: 09:37‑09:42
(5+1 min)
 Neuromorphic computing with BrainScaleS: accelerated analog spiking neural network emulation show presentation.pdf (public accessible)

.ics

Eric Müller (Ruprecht-Karls-Universitaet Heidelberg)
CET: 10:43‑10:48
UTC: 09:43‑09:48
(5+1 min)
 Neurorobotics: connect brain models to embodied agents interacting with a simulated environment

.ics

Fabrice Morin
CET: 10:49
UTC: 09:49
Introductions: coupling of simulators
CET: 10:49‑10:54
UTC: 09:49‑09:54
(5+1 min)
 MUSIC: a tool for co-simulation show presentation.pdf (public accessible), show talk video

.ics

Mikael Djurfeldt (Kungliga Tekniska Hoegskolan)
CET: 10:55‑11:00
UTC: 09:55‑10:00
(5 min)
 Co-sim show presentation.pdf (public accessible)

.ics

Wouter Klijn
CET: 11:00‑11:30
UTC: 10:00‑10:30
(30 min)
 Break
CET: 11:30
UTC: 10:30
Introductions: High Performance Computing
CET: 11:30‑11:40
UTC: 10:30‑10:40
(10+2 min)
 HPC
video (restricted access)
  • CINECA HPC
    • Scalable Compute on Galileo100 platform
    • HPC Cloud Computing infrastructure at CINECA
    • BURST buffering
  • Central Data Transfer Services

.ics

Lena Oden (Forschungszentrum Juelich GmbH)
CET: 11:42
UTC: 10:42
Other
CET: 11:42‑11:47
UTC: 10:42‑10:47
(5+1 min)
 Health Data Cloud: processing with data protection by design and by default

.ics

Petra Ritter
CET: 11:48‑11:53
UTC: 10:48‑10:53
(5+1 min)
 Elephant: represent and work with electrophysiological activity data

.ics

Michael Denker (Forschungszentrum Juelich GmbH)
CET: 12:00
UTC: 11:00
The EBRAINS Collaboratory
CET: 12:00‑13:00
UTC: 11:00‑12:00
(60 min)
 Introduction to the EBRAINS Collaboratory: hands-on for newcomers show presentation.pdf (public accessible), show talk video

Links:

Introduction to the EBRAINS Collaboratory

We will present the services included : identifying users, permissions, wiki pages, storage in Drive and Bucket, Office collaborative editing, sharing files, and a very short intro to the Lab for running Jupyter notebooks. This will include a small hands-on for users to try out the basic features.

.ics

Paul Chaney (EBRAINS AISBL)
CET: 13:00‑14:00
UTC: 12:00‑13:00
(60 min)
 Lunch
CET: 14:00‑15:30
UTC: 13:00‑14:30
(90 min)
 Collaboratory Lab for Jupyter notebooks show presentation.pdf (public accessible), video (restricted access)

Links:

show abstract

.ics

Paul Chaney (EBRAINS AISBL)
CET: 15:30‑16:00
UTC: 14:30‑15:00
(30 min)
 Break
CET: 16:00‑17:30
UTC: 15:00‑16:30
(90 min)
 Collaboratory services for tool and service developers show presentation.pdf (public accessible)

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

Links:

show abstract

.ics

Paul Chaney (EBRAINS AISBL)

Wednesday, 9 November 2022
CET: 09:00
UTC: 08:00
Simulate with EBRAINS: parallel tools hands-on sessions

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

CET: 09:00‑11:00
UTC: 08:00‑10:00
(120 min)
Hands-on sessions in parallel
  • 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.

show abstract

Session 1: NEST DesktopSession 2Session 3
Sebastian Spreizer (Universität Trier)
Petra Ritter (Charite - Universitaetsmedizin Berlin)

TVB

Tanguy Damart (Swiss Federal Institute of Technology in Lausanne (EPFL))

Electrical model building toolset

.ics

CET: 11:00‑11:30
UTC: 10:00‑10:30
(30 min)
Break
CET: 11:30‑13:00
UTC: 10:30‑12:00
(90 min)

  • 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

show abstract

Session 1: NESTMLSession 2Session 3Session 4: PyNN
Charl Linssen (Forschungszentrum Juelich GmbH)

show talk video

TVB (continued)


Electrical model building toolset (continued)

Andrew Davison (Centre National de la Recherche Scientifique)

description for the hands-on session


show talk video

.ics

CET: 13:00‑14:00
UTC: 12:00‑13:00
(60 min)
Lunch
CET: 14:00‑16:00
UTC: 13:00‑15:00
(120 min)
Hands-on sessions in parallel
  • 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

show abstract

Session 1: NeuronHealth Data CloudSession 3: ArborSession 4: MUSIC
Robert McDougal

show talk video
CoreNEURON
Pramod Shivaji Kumbhar (Swiss Federal Institute of Technology in Lausanne (EPFL))
Petra Ritter (Charite - Universitaetsmedizin Berlin)
Brent Huisman (Forschungszentrum Juelich GmbH)
Mikael Djurfeldt (Kungliga Tekniska Hoegskolan)


slides

.ics

CET: 16:00‑16:30
UTC: 15:00‑15:30
(30 min)
Break
CET: 16:30‑18:30
UTC: 15:30‑17:30
(120 min)
Hands on (parallel) sessions
Session 1 (dial in)Session 2 (dial in)Session 3 (dial in)Session 4
SpiNNaker
(Andrew Rowely)
Health Data Cloud (cont.)SSB toolkit
(Rui Ribeiro)
-


  • SSB toolkit: from molecular structure to subcellular networks
  • SpiNNaker: Hands-on the SpiNNaker Neuromorphic platform, writing basic neural networks using PyNN via Jupyter.

show abstract

.ics


Thursday, 10 November 2022
CET: 09:00
UTC: 08:00
Simulate with EBRAINS: parallel tools hands-on sessions

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

CET: 09:00‑11:00
UTC: 08:00‑10:00
(120 min)
Hands on (parallel) sessions
  • 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.

show abstract

Session 1: Central Data Transfer ServicesSession 2: Macromolecular flexibility databasesSession 3: Neurorobotics Platform
Shiting Long (Forschungszentrum Juelich GmbH)

Provided material
(Shiting Long and Miguel Eduardo Carpio Miranda)

Adam Hospital (Institute for Research in Biomedicine Barcelona)

Provided material

Fabrice Morin (Technische Universitaet Muenchen)

Neurorobotics Platform (NRP)
Provided material

.ics

CET: 11:00‑11:30
UTC: 10:00‑10:30
(30 min)
Break
CET: 11:30‑13:00
UTC: 10:30‑12:00
(90 min)
Hands on (parallel) sessions

show abstract

Scalable Compute on Galileo100 platformτ-RAMD
Susana Bueno Minguez (Italian National Supercomputing Consortium)
Diego Molinari (Italian National Supercomputing Consortium)

information on how to get a budget and use the system

show presentation.pdf (only with login + special group membership)
Giulia D'Arrigo (HITS gGmbH)

Estimation of residence time and determination of unbinding pathways through τ-Random Acceleration Molecular Dynamics (τ-RAMD)

.ics

CET: 13:00‑14:00
UTC: 12:00‑13:00
(60 min)
Lunch
CET: 14:00‑16:00
UTC: 13:00‑15:00
(120 min)
Hands on sessions in parallel:

show abstract

HPC Cloud Computing infrastructure at CINECAMiMiCBrainScaleS - hands on introduction
Giuseppa Muscianisi (Italian National Supercomputing Consortium)
HPC Interactive Computing infrastructure at CINECA
Fabio Pitari (Italian National Supercomputing Consortium)

show talk video
Davide Mandelli (Forschungszentrum Juelich GmbH)
Mirko Paulikat (Forschungszentrum Juelich GmbH)
Bharath Raghavan (Forschungszentrum Juelich GmbH)


Instructions for Participants to Access to HPC resources


show talk video
Christian Mauch (Ruprecht-Karls-Universitaet Heidelberg)

show talk video
BrainScaleS - training with the Superspike Rule
Johannes Weis (Ruprecht-Karls-Universitaet Heidelberg)

show talk video
BrainScaleS -- Plasticity and structured neurons
Jakob Kaiser (Ruprecht-Karls-Universitaet Heidelberg)

show talk video

.ics

CET: 16:00‑16:30
UTC: 15:00‑15:30
(30 min)
Break
CET: 16:30‑18:30
UTC: 15:30‑17:30
(120 min)
Hands on (parallel) sessions
  • BURST buffering: BURST buffering: how to benefit from a fast data tier
  • Elephant: a data analysis frmework for electrophysiological activity data

show abstract

Session 1: BURST bufferingSession 2Session 3: Elephant
Andrea Pieretti (Italian National Supercomputing Consortium)

MiMiC (cont.)

Moritz Kern (Forschungszentrum Juelich GmbH)
Michael Denker (Forschungszentrum Juelich GmbH)

.ics

CET: 19:00
UTC: 18:00
End of the event "Simulate with EBRAINS"