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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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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

The event is free of charge, but registration is necessary.

  • An EBRAINS account (free of charge as well) is needed to register. To get an EBAINS account, please use ebrains.eu/register
  • Then please register here
  • The dial-in information for the zoom video conference will be sent to the registered participants shortly before the event

Venue: Online

The training event will happen as an online zoom video conference = can be attended without the need to travel.

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

For capacity planning we are going to ask the registered attendants, which sessions they plan to attend.

Time zone

Times in the agenda are by default in CET (Europe, Berlin) and UTC.

To show different time zones: Africa (UTC, Western-, Central- and Eastern-African Time zones), America (Pacific-, Mountain-, Central- and Eastern-Time), Australia, China, India, . Japan, .. or only CET ...

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.

CET: 09:00‑10:30
UTC: 08:00‑09:30
(90 min)
 FURMS & Fenix AAI (I)
CET: 10:30‑11:00
UTC: 09:30‑10:00
(30 min)
 Break
CET: 11:00‑12:30
UTC: 10:00‑11:30
(90 min)
 FURMS & Fenix AAI (II)
CET: 12:30‑13:30
UTC: 11:30‑12:30
(60 min)
 Lunch
CET: 13:30‑15:30
UTC: 12:30‑14:30
(120 min)
 FURMS & Fenix AAI (III)
CET: 15:30‑16:00
UTC: 14:30‑15:00
(30 min)
 Break
CET: 16:00‑18:00
UTC: 15:00‑17:00
(120 min)
 FURMS & Fenix AAI (IV)

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).

CET: 09:00‑09:05
UTC: 08:00‑08:05
(5 min)
Welcome
CET: 09:05‑09:25
UTC: 08:05‑08:25
(20+5 min)
EBRAINS for YOUR researchKatrin 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
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
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.
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)Petra Ritter (Charite - Universitaetsmedizin Berlin)
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
CET: 10:37‑10:42
UTC: 09:37‑09:42
(5+1 min)
 Neuromorphic computing with BrainScaleS: accelerated analog spiking neural network emulation
CET: 10:43‑10:48
UTC: 09:43‑09:48
(5+1 min)
 Neurorobotics: connect brain models to embodied agents interacting with a simulated environmentFabrice Morin (Technische Universitaet Muenchen)
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
CET: 10:55‑11:00
UTC: 09:55‑10:00
(5+1 min)
 Co-sim (pending)
CET: 11:01‑11:31
UTC: 10:01‑10:31
(30 min)
 Break
CET: 11:31
UTC: 10:31
Introductions: High Performance Computing
CET: 11:31‑11:41
UTC: 10:31‑10:41
(10+2 min)
 
  • CINECA HPC
    • Scalable Compute on Galileo100 platform
    • HPC Cloud Computing infrastructure at CINECA
    • BURST buffering
  • Central Data Transfer Services
Lena Oden (Forschungszentrum Julich GmbH)
CET: 11:43
UTC: 10:43
Other
CET: 11:43‑11:48
UTC: 10:43‑10:48
(5+1 min)
 Health Data Cloud: processing with data protection by design and by default Petra Ritter (Charite - Universitaetsmedizin Berlin)
CET: 11:49‑11:54
UTC: 10:49‑10:54
(5+1 min)
 Elephant: represent and work with electrophysiological activity data
CET: 11:55
UTC: 10:55
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 abstract

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 abstract

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

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

show abstract


Wednesday, 9 November 2022
CET: 09:00
UTC: 08:00
Simulate with EBRAINS: NEST and arbor simulators, TVB, Health data cloud, Neuromorphic Computing, Electrical model buidling toolset
CET: 09:00‑11:00
UTC: 08:00‑10:00
(120 min)
Hands-on sessions in parallel
Session 1Session 2Session 3Session 4
NEST DesktopTVBElectrical model building toolset-


  • 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
  • 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

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)

Session 1Session 2Session 3Session 4
NESTMLTVB (continued)Electrical model building toolset (continued)PyNN


  • 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

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
Session 1Session 2Session 3Session 4
Neuron / CoreNEURONHealth Data Cloud Arbor MUSIC


  • 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).
  • 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

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 1Session 2Session 3Session 4
-Health Data Cloud (cont.)SSB toolkitSpiNNaker


  • 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


Thursday, 10 November 2022
CET: 09:00
UTC: 08:00
EBRAINS simulation, NMC and HPC, day IV
CET: 09:00‑11:00
UTC: 08:00‑10:00
(120 min)
Hands on (parallel) sessions
Session 1Session 2Session 3
Central Data Transfer ServicesMacromolecular flexibility databasesNeurorobotics Platform (NRP)


  • Central Data Transfer Services: data transfer in Fenix
  • 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

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
Session 1Session 2Session 3
Scalable Compute on Galileo100 platformτ-RAMDCo-Sim


  • Scalable Compute on Galileo100 platform: information on how to get a budget and use the system
  • τ-RAMD: Estimation of residence time and determination of unbinding pathways through τ-Random Acceleration Molecular Dynamics (τ-RAMD)
  • Co-Sim: co-simulation, connecting several different simulation, analysis and visualization engines

show abstract

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:
Session 1Session 2Session 3
HPC Cloud Computing infrastructure at CINECAMiMiCBrainScaleS


show abstract

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 1Session 2Session 3
BURST bufferingMiMiC (cont.)Elephant


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

show abstract

CET: 19:00
UTC: 18:00
End of the event