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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:

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.

.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:

We will present how to:

  • use IAM for user authentication (for services),
  • use the quota manager (for services),
  • deploy tools to the Lab environment,
  • using the INTegration environment for testing This will include some time for open discussion with attendees.

.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.
Session 1: NEST DesktopSession 2Session 3
Sebastian Spreizer (Universität Trier)

NEST Desktop

NEST Desktop is a web-based graphical user interface (GUI) for the NEST Simulator. The GUI guides users to understand the script code for NEST Simulator. The aim of NEST Desktop is an application which should be intuitive and easy to learn for newcomers, but also attractive for experienced users to perform sophisticated simulations.

In this session, we will learn typical steps of a virtual experiment with spiking network model:

  • Construct a network of neurons and I/O devices
  • Modify models and parameters
  • Learn the simulation code
  • Analyze spiking activity or analog signals, e.g. membrane potentials
  • Manage projects and event data.

By the end of the session we will demonstrate the concept of the client-server architecture in which NEST Desktop is the client and NEST Simulator is the backend server.

Petra Ritter (Charite - Universitaetsmedizin Berlin)

TVB

TVB

We demonstrate the TVB-EBRAINS integrated end-to-end personalized brain simulation workflows in the Cloud (Schirner et al. 2022) that can be reached via EBRAINS The Virtual Brain Cloud: https://ebrains.eu/service/the-virtual-brain/. Attendees can work jointly in a dedicated collaboratory during the hands-on-session.

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

Electrical model building toolset

Electrical model building toolset

In this session, you will build a biologically detailed neuron model using the NEURON simulator and three open source python packages: eFEL, BluePyEfe and BluePyOpt. First, a short lecture will describe the process of extraction of electrical features from experimental patch-clamp recordings as well as the algorithms used for the creation of the numerical models. Then, during a hands-on session, biological data will be made available and will be used as target for the creation of one or several electrical neuron models.

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

NESTML

NESTML is a domain-specific language for neuron and synapse models. These dynamical models can be used in simulations of brain networks on several platforms, in particular NEST Simulator. NESTML combines an easy to understand, yet powerful syntax with a flexible processing toolchain, written in Python, and good simulation performance by means of code generation (C++ for NEST Simulator).

In this tutorial, you will get hands-on experience creating new neuron and synapse models, instantiating them in a NEST simulation, and doing analysis on the recorded data. We will cover creating a compartmental neuron model with an active dendrite, adding stochasticity to a model, and several synaptic plasticity models such as spike-timing dependent plasticity (STDP) and third-factor plasticity rules.


show talk video

TVB (continued)


Electrical model building toolset (continued)

Andrew Davison (Centre National de la Recherche Scientifique)

description for the hands-on session

Using the PyNN library to build and simulate spiking neural network models on EBRAINS

PyNN is a simulator-independent Python library for building neuronal network models. Models built with the PyNN API can be simulated without any code modifications on any simulator that PyNN supports (currently NEURON, NEST, and Brian), and on the SpiNNaker and BrainScaleS neuromorphic hardware systems. This allows users to:

  • Perform simulations on laptops, supercomputers or neuromorphic hardware with the same code
  • Build complex models with minimal code
  • More easily migrate models between different simulators and from simulators to neuromorphic computing systems
  • Cross-check your simulation results on different simulators In this hands-on session, we will introduce the concepts behind PyNN and together build and simulate spiking network models on the EBRAINS Jupyter Lab service.

Participants will learn how to access different simulation tools in the EBRAINS Lab; how to build spiking network models with PyNN, how to run simulation experiments with NEST, NEURON, Brian and SpiNNaker, and how to visualize the results.


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

Neuron / CoreNEURON

The NEURON simulation environment is used in laboratories and classrooms around the world, for building and using computational models of neurons and networks of neurons. CoreNEURON is a compute engine for the NEURON simulator, optimised for both memory usage and computational speed, and designed to target modern hardware architectures. Additionally, NEURON and CoreNEURON are now also available in a new, single pip-based installation, giving Python users easy and accessible usage of this improved simulation package.

In this session we will present to EBRAINS users via the Collaboratory:

  1. An introduction of NEURON and its API to build single cell and network models and

Level: Beginner to Intermediate.


show talk video
CoreNEURON
Pramod Shivaji Kumbhar (Swiss Federal Institute of Technology in Lausanne (EPFL))

In this session we will present to EBRAINS users via the Collaboratory: 2) How to adapt and run existing models with CoreNEURON for speed on CPU/GPU platforms. EBRAINS users are encouraged to bring their models to try and apply the lessons to their use cases and receive help from the presenters.

Level: Beginner to Intermediate.

Petra Ritter (Charite - Universitaetsmedizin Berlin)

Health Data Cloud

This session will provide an introduction to EBRAINS Service for Sensitive Data - the Health Data Cloud (HDC). We will demonstrate the technical and organizational measures to provide data protection by design and by default according to the EU general data protection regulations (GDPR). Features such as the GUI, command line interface, gateway to HPC, workbench tools, etc. will be demonstrated. We also plan a hands on session where attendees can experience HDC functionality on their own.

Brent Huisman (Forschungszentrum Juelich GmbH)

Arbor

Arbor is a portable, high-performance library for computational neuroscience simulations with multi-compartment, morphologically-detailed cells, ranging from single cell models to very large networks. Optimisations make Arbor an order of magnitude faster than the most widely-used comparable simulation software. Download Arbor as a C++ library and integrate it in your own program, or install it as a Python library (through pip) and import in any Python script.

Mikael Djurfeldt (Kungliga Tekniska Hoegskolan)


slides

MUSIC

MUSIC is a tool for co-simulation in the computational neuroscience domain. It supports simulations where different parts of a model is simulated by different instances of a simulator or different simulators and/or other software or hardware. MUSIC supports large-scale simulations on clusters but can be run on a desktop or laptop as well.

In this session, participants will be introduced to the PyNN/MUSIC interface which allows MUSIC co-simulations to be specified by a single PyNN script. Co-simulations involving NEST and NEURON as well as SpiNNaker and a virtual environment will be demonstrated.

.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.

SSB toolkit

from molecular structure to subcellular networks

The attendees will learn how to use structural biological data to simulate mathematical models of signal-transductions pathways of GPCRs to predict individual drug response phenotypes by correlating molecular interactions with cellular functions.

SpiNNaker

Hands-on session on the SpiNNaker neuromorphic compute system

.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.
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)

Central Data Transfer Services

This session is dedicated to introduce the Data Transfer service in FENIX and explain its usage in different scenarios. It will include a short presentation and demos of Swift-to-Swift data transfers using the DT service, with a possibility to provide hands-on experience to users.

Adam Hospital (Institute for Research in Biomedicine Barcelona)

Provided material

Macromolecular flexibility databases; Setting up & running Molecular Dynamics (MD) simulations

The session will present and describe macromolecular flexibility databases integrated in the EBRAINS infrastructure (MoDEL-CNSCNS ligandsBioExcel-CV19), built from information extracted from Molecular Dynamics (MD) simulations. The hands-on session will be focused on setting up and running a MD simulation.

Fabrice Morin (Technische Universitaet Muenchen)

Neurorobotics Platform (NRP)
Provided material

Neurorobotics

The Neurorobotics Platform (NRP) is a set if software tools that was specifically developed to enable its users to connect brain models to embodied agents interacting with a simulated environment. V4.0 of the NRP emphasizes its function as an integrative ecosystem capable of orchestrating multiple simulation engines and heterogeneous control components in a distributed manner. This session will introduce NRP v4.0 and showcase how it can be used for multi-engine simulations, learning experiments, and soft real-time simulations.

.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
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

Scalable Compute on Galileo100 platform

During this session we will provide an overview of Galileo100 cluster available at CINECA and information for its usage. Following general details on how to request a budget, the access mode, the on-line documentation and the support provided, we will describe the main harwdware caracteristics of this cluster and provide information on the available storage spaces. We will also describe the programming environment, focusing on main compilers and libraries available, and we will provide an overview of the production environment, focusing on main applications available (modules environment), the scheduling of jobs and the budget consumption. At last, benchmarks results performed on Cascadelake architecture with usual HBP codes will be shown.

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)

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

The determination of binding kinetic parameters, and particularly of dissociation rates, is of high interest for compound optimization in structure-based drug discovery as well as for modelling complex signaling cascades. τ-RAMD is a computationally efficient tool that enables the estimation of residence time of molecular partners. In this session, lecture and hands-on session on the use of RAMD simulations for estimating dissociation rates of protein-ligand and protein-protein complexes by the τRAMD procedure will be given.

.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:
HPC Cloud Computing infrastructure at CINECAMiMiCBrainScaleS - hands on introduction
Giuseppa Muscianisi (Italian National Supercomputing Consortium)

HPC Cloud Computing infrastructure at CINECA

After a brief overview of the HPC Cloud Computing infrastructure available at CINECA, it will be shown how to access and use it. All the participants will be provided with the possibility to test the infrastructure by configuring and launching their own virtual machine also.

HPC Interactive Computing infrastructure at CINECA
Fabio Pitari (Italian National Supercomputing Consortium)

HPC Interactive Computing infrastructure at CINECA (1h)

This is a brief overview of the framework that Cineca adopted as interactive computing interface. A short summary of the Jupyterlab capabilities will be shown, and a particular focus will be kept on its interaction with the HPC environment and with the scheduler. The user experience allowed by the infrastructure and the adopted plugins will be presented, in different use case scenarios.


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

MiMiC: Mutiscale QM/MM simulations of ligand-enzyme complex with MiMiC

This hands-on session will provide participants with theoretical background on multiscale QM/MM simulations and practical experience using the highly scalable MiMiC code to investigate neurobiologically relevant systems runnning on high-end HPC facilities.


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

BrainScaleS

Hands-on tutorial with information on the first steps to run a PyNN described network interactively on the BrainScaleS systems up to defining and using structured neurons.


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

BURST buffering

A brief introduction to CINECA's burst buffered storage service. During the hands-on session participants will have the opportunity to see how to benefit from a fast data tier for I/O-intensive applications.


MiMiC (cont.)

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

Elephant

In this workshop, we will explore how to represent and work with electrophysiological activity data consisting of spiking activity and local field potentials using the Neo data model, and how to perform a statistical analysis of such data using the Elephant framework. We will work with a publicly available electrophysiological dataset to walk-through a potential data analysis scenario step-by-step from loading the data to obtaining results on the statistical characterization of spiking activity using a series of prepared Jupyter notebooks.

.ics

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