The BrainModes Visualiser
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Brain simulation helps us understanding how our brain works – and developing personalized therapies for its diseases.

A human brain consists of 86 billion neurons and 150 trillion connections between them. It runs on as little energy as an LED light bulb. It would take 1,500 Google data centers (they only have 15) to simulate just one brain with molecular accuracy, costing 1 trillion dollar per year and consuming 600 terawatt hours.

Here at the Brain Simulation Section (part of Charité Universitätsmedizin Berlin), we have been at the forefront of network-based brain simulation, computational neuroscience and its clinical application for more than 10 years.

In collaboration with other international research centers, we have developed a way to simulate a brain even on a laptop – with reduced complexity but feasible, sufficiently accurate, scalable and already used in practical clinical applications.

We work towards our vision of providing digital copies of a person’s brain to virtually plan and test personalized treatment of brain orders, e.g. Alzheimer’s, stroke, epilepsy or tumors.

Our team is growing fast and we would be happy to welcome you, e.g. as software developer, lab manager or research assistant! Check out our current job openings or send us your speculative application!

portrait photo

Brain Simulation Section is a research center of Charité Universitätsmedizin

Latest activities

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  • university-vienna

    TVB Cloud Webinar on data sharing in health research

    May 20

    Our EU Project Virtual Brain Cloud recently held a webinar organized by our partner University Vienna Department of Innovation and Digitalisation in Law on Data Sharing in Health Research.

    You can find the recording of the webinar on the University Vienna Department of Innovation and Digitalisation in Law's YouTube channel:


    Topics covered in the webinar include:

    • Personal data sharing challenges in research projects (Forgó)

    • Legal Framework - Data Protection Concepts relevant for data sharing (Johnson)

    • TVB-Cloud Project Data Sharing Steps (Rissetto)

    • TVB-Cloud Project Data Sharing Contractual Structures (Cepic)

  • TVB Flyer EBRAINS inside pages

    The Virtual Brain on EBRAINS

    May 14

    The Virtual Brain (TVB) on EBRAINS is a large ecosystem of tools for constructing, simulating and analyzing brain network models. The Virtual Brain tool set can be used for end-to-end personalized brain simulation. It is completely integrated in the EBRAINS technical infrastructure.

    The Virtual Brain integration in EBRAINS allows users to have a seamless end-to-end experience of personalized brain model creation and multi-scale brain simulation using high-performance computing on the cloud. This makes it possible to process large cohort datasets in order to produce generalized results - a precondition for clinical translation.

    The Virtual Brain (TVB) ecosystem includes:

    The Virtual Brain pipeline

    TVB pipeline is a neuroimaging pipeline that extracts structural and functional connectomes from MRI data to personalize brain models.

    TVB+NEST

    TVB+NEST is a Python toolbox that makes it easier to simulate multi-scale networks. Multi-scale networks simulate both activity on a coarse scale and activity on a finer scale. Essentially, TVB+NEST is a Python wrapper for The Virtual Brain neuroinformatics platform and the NEST spiking network simulator.

    Fast_TVB

    Fast_TVB is thousands of times faster than Python TVB as it uses several optimization techniques and is implemented in the hardware-near language C. In addition, users can specify the number of threads that will process data simultaneously across multiple processors, as is often done on supercomputers.

    Disease Models

    An advanced application of TVB is the specification of disease models. This is done using a workflow that augments TVB with empirical PET data.

    Tumor Brain Models

    Tumor Brain Models is a data set that includes structural and functional connectomes from brain tumor patients and healthy control subjects.

    INCF training space

    A dedicated INCF training space provides didactic use cases and Jupyter notebooks to get new users up to speed. EduCases demonstrate - for example - how to use TVB via the Collaboratory of the Human Brain Project, how to run multi-scale co-simulations with other simulators such as NEST and how to process imaging data to construct personalized virtual brains of healthy individuals and patients.

    The Virtual Brain simulator

    The Virtual Brain simulator is the main TVB software package. It is a neuroinformatics platform that provides an ecosystem of tools for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivity. TVB can be operated via GUI and programmatic Python interface. The Virtual brain simulator is accessible via EBRAINS user accounts.

    Check out a detailed step by step guide to using The Virtual Brain tools for end-to-end personalized brain simulation here.

  • vre-video-still

    BiH/Charité Virtual Research Environment

    May 12

    We are excited to announce the development of the BIH/Charité Virtual Research Environment. The Virtual Research Environment (VRE) integrates with the Charité Health Data Platform (HDP) systems, which are responsible for ingesting patient data from the Charité hospital and making it available for use in research.

    The goal of the VRE is to make it easier for researchers to find and securely access data and use it in innovative ways. It will extend the Health Data Platform by providing:

    • workflows for radiologic imaging data
    • a model for cataloguing data and making it easier to find
    • workbenches for modelling, simulating and analyzing data and
    • a portal that is open also for external users who do not belong to Charité

    The VRE will be interoperable with international open health data initiatives, such as the Virtual Brain Cloud or the Human Brain Project EBRAINS platform or the European Open Science cloud.

    The development of the Virtual Research Environment will follow the FAIR guiding principles for scientific data management - Findability Accessibility Interoperability Reusability. We want to ensure that this development is open and accessible to all clinicians and scientists at Charité and BIH so we can solve today's pressing medical challenges together!


    Both the Health Data Platform and the Virtual Research Environment are projects of the BIH Translation Hub Digital Medicine. To find out more details please visit the Virtual Research Environment project page here.

  • Video 2 from Identifying optimal working points of individual Virtual Brains

    New paper on identifying optimal working points of individual Virtual Brains

    March 27

    Our new preprint Optimal working points of individual Virtual Brains is out! You can read it here.

    With our international colleagues, we used The Virtual Brain simulation platform, to explore 50 individual adult human brains (ages 18-80). We investigated how personalized connectome-based brain network modelling captures various empirical observations as measured by functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). We systematically explored the role of conduction velocity, global coupling and graph theoretical features of individual SCs.

    Our results are twofold:

    Firstly, for each individual brain we identified a converging parameter subspace that yielded realistic brain activity:

    • topology of resting-state fMRI functional connectivity (FC)
    • functional connectivity dynamics (FCD)
    • electrophysiological oscillations in the delta (3-4 Hz) and alpha (8-12 Hz) frequency range and their bi-modality low and high energy modes.

    We only see biologically realistic mode switching in the global network when the local model is in a bistable regime.

    Secondly, our simulations reveal the explicit network mechanisms that lead to electrophysiological oscillations, their bimodal behaviour and inter-regional differences.

Meet our team

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  • Educational Course at OHBM 2020

    26

    Jun

    Montreal, Canada

    The following events will now take place online!

    Please join our educational course Fundamental Concepts and Methods in Network Neuroscience at OHBM 2020 in Montreal on the 26th of June.

    Fundamental Concepts and Methods in Network Neuroscience Workshop

    This workshop - organized by Dr. Alex Fornito - will cover essential aspects of constructing networks, such as how to define network nodes and measure diverse aspects of structural and functional connectivity. It will teach attendees critical considerations in the statistical analysis of connectomes and how to integrate brain imaging measures with other diverse kinds of data, such as those relating to cytoarchitecture, gene expression, and connectivity in other species. The workshop will also explain key concepts and measures, such as network communities, centrality and hubs, and models of communication processes and dynamics.

    Key Learning Outcomes of the Workshop

    • the strengths and weaknesses of different methods for parcellating the brain and defining network nodes;
    • how to quantify and interpret different measures of structural and functional connectivity;
    • how to define network communities and hubs, characterize communication processes on networks, and respect limitations of current analytic methods;
    • appropriate techniques for statistical inference on networks;
    • how to use both graph theoretic and biophysical models of brain network dynamics; and
    • how to conduct multimodal analyses to gain greater insight into network organization

    About OHBM 2020

    The Organization for Human Brain Mapping (OHBM) is an international society dedicated to using neuroimaging to discover the organization of the human brain. Other speakers at this year's annual meeting include:

    • Dr Petra Ritter (Director of the Brain Simulation Section at Charité Universitätsmedizin Berlin).
    • Dr Richard Betzel (Assistant Professor of Psychological and Brain Sciences at Indiana University)
    • Dr Andrew Zalesky (Associate Professor and National Health and Medical Research Council (NHMRC) Senior Research Fellow at the University of Melbourne).

    Online Program

    The education course Fundamental Concepts and Methods in Network Neuroscience will run all day from 08.00 to 16.30. You can find the rest of the program here.

    Online Registration

    You can register for the 2020 Annual Meeting here.

  • POSTPONED: Brain Connectivity Workshop 2020 to be held in Toronto, Canada

    21

    Jun

    Toronto, Canada

    This event has been postponed until next year.

    The aim of Brain Connectivity Workshop is to establish a dialogue between researchers in computational neuroscience, neuroscience methodology and experimental neuroscience about the emerging field of brain connectivity.

    This year the workshop will revisit the first ever Brain Connectivity workshop theme from a different perspective: "What does the mind think of the brain?" - focusing the discussions around what we have learned about our mind over the last 20 years of brain connectomics.

    The topics will deal with consciousness and cognition, looking at the tripartite relationship between anatomical connectivity, brain dynamics and cognitive function.

    The Brain Connectivity Workshop is conveniently right before OHBM in Montreal, Canada (June 26-30).

    Registration

    Tickets for this workshops are limited. You can buy tickets for $350 CAD online.

    Tentative list of speakers

    Please check for updates about confirmed speakers on more details von the BCW2020 event website.

    • Giulio Tononi: Consciousness & Cognition

      University of Wisconsin - Madison

    • Andreea Diaconescu: Bayesian models of Psychiatric Disorders

      University of Toronto

    • Viktor Jirsa: Dynamical Systems

      Aix Marseille University

    • Michael Mack: Cognitive Modeling

      University of Toronto

    • Bratislav Misic: Graphs/Networks

      McGill University

    • Petra Ritter: Multiscale Imaging/Modeling

      Charite University

    • Lisa Barrett: Brain-Body Interactions & Allostasis

      Northeastern University

    • Dani Bassett: Network Control Theory

      University of Pennsylvania

    • Gustavo Deco: Network Architectures in Cognition

      Pompeu Fabra University

    • Athena Demertzi: Conscious & Unconscious States

      University of Liege

    • Emily Finn: Fingerprinting Connectivity & Cognition

      Dartmouth College

    • Mike Halassa: Thalamocortical Interactions in Cognition

      Massachusetts Institute of Technology

    • Biyu Jade He: Perceptual Awareness

      New York University

    • Randy McIntosh: Hidden Repertoires in Cognition

      University of Toronto

    • Rosalyn Moran: Bayesian Models, Free Energy

      Kings College London

    • Mac Shine: Modulation of Network Dynamics

      University of Sydney

    • Enzo Tagliazucchi: Consciousness and Entropy

      University of Buenos Aires

    • Brandon Turner: Integration of Cognition and Neural Models

      Ohio State University

  • CANCELLED: Join us in Calgary and Lethbridge (Canada) for 2 lectures and a workshop on The Virtual Brain!

    17

    Mar

    Lethbridge and Calgary, Canada

    The following events have been cancelled.

    In March 2020 Dr. Petra Ritter, Dr Paul Triebkorn and Jan Stansinski MSc will present two lectures and a workshop on The Virtual Brain in Lethbridge & Calgary, Canada

    2020 Harley Hotchkiss Memorial Lecture

    Dr. Petra Ritter will hold a lecture on The Virtual Brain simulation platform: Inferring principles of network interactions underlying cognition at the Canadian Centre for Behavioural Neuroscience on March 17th.

    Time

    March 17, 2020 @ 12:15pm

    Location

    University of Lethbridge
    Canadian Centre for Behavioural Neuroscience
    Room SA8002

    Realise Module: The Virtual Brain Workshop

    The Virtual Brain (TVB) is a large-scale simulation platform that enables biologically realisticmodeling of the network dynamics of the human brain. Join Dr. Petra Ritter, and Dr. Paul Triebkorn and Jan Stasinski, MSc for a hands-on introduction to the platform.
    Find out more details and register here.

    Time

    March 18, 1:00 to 4:30 pm
    March 19, 8:30 to 11:30 am

    Location

    University of Calgary

    HBI Seminar Series

    Dr. Petra Ritter will give a lecture at the University of Calgary as a part of the Hotchkiss Brain Institute Seminar Series

    Time

    March 20, 2020
    12:00pm - 1:00pm MDT (19:00 - 20:00 CEST)

    Location

    Sign up for notifications about seminars in the HBI series here.

  • The Virtual Brain Node#10 Workshop

    9

    Mar

    Berlin, Germany

    The TVB Berlin team is organizing The Virtual Brain Node#10 Workshop: Personalized Multi-Scale Brain Simulation on March 9-12, 2020, in Berlin.

    This new node is an official (elective) course of the Bernstein Center for Computational Neuroscience Berlin. 2 ECTS are awarded upon successful completion of the course.

    This workshop provides basic knowledge on personalized brain network modeling. Required interdisciplinary methods will be introduced. A focus will be set on the open-source simulation platform The Virtual Brain (TVB), and basic concepts and methods will be introduced. Participants will gain theoretical knowledge and subsequently, use this knowledge to construct brain models, process multimodal neuroimaging data for creating individual brain, run simulations and use supporting neuroinformatics tools such as collaboratories, pipelines, workflows and data repositories. Participants will be able to operate the neuroinformatics platform TVB. The following topics will be covered:

    • Theoretical background of large-scale brain network modeling and concepts of nonlinear dynamics (bifurcation analysis, phase plane, flows on manifolds)

    • Architecture of TVB simulator

    • Interacting with TVB using GUI and CLI

    • Modeling resting-state networks activity in human, mouse, and macaque brain

    • Parameter optimization and model inference

    • Visualization of multimodal brain dynamics

    • Application of brain network modeling for clinical questions such as in epilepsy

    • Multiscale co-simulation using TVB and microscopic simulators such as NEST

    • Personalization pipelines: processing of brain images (MRI, fMRI, DTI, PET) and electrophysiological data (EEG, MEG) for individualization of brain network model

    • Running workflows on high performance computers (HPC)

    • Making use of and contributing to collaborative informatics simulation platforms such as Human Brain Project’s EBRAINS

    Preliminary Program

    The workshop consists of 4 full-day sessions:

    March 9, Conference Room 1

    • 09:00 - 10:30

      Introduction to The Virtual Brain (TVB) simulation platform (Lecture)

    • 10:30 - 11:30

      Architecture of TVB (Lecture)

    • 11:30 - 13:00

      Neural population models in TVB and Phase Plane Viewer (Lecture)

    • 13:00 - 14:00

      Lunch break

    • 14:00 - 15:00

      Import TVB ready data to TVB and create a brain model (Tutorial)

    • 15:00 - 16:00

      My first simulation (Tutorial)

    • 16:00 - 18:00

      The Virtual Mouse Brain (TVMB): Simulate a mouse brain network model (Tutorial)

    March 10, Conference Room 1

    • 09:00 - 10:00

      Bridging multiscale in TVB (Lecture)

    • 10:00 - 12:00

      Perform a multiscale co-simulation with TVB-NEST (Tutorial)

    • 12:00 - 13:00

      Generate a macaque brain model (Tutorial)

    • 13:00 - 14:00

      Lunch break

    • 14:00 - 16:00

      Surface-based simulation (Tutorial)

    • 16:00 - 18:00

      Perform a brain stimulation (Tutorial)

    March 11, Conference Room 1

    • 09:00 - 11:30

      Generating TVB ready imaging data (Lecture)

    • 11:30 - 13:00

      Operating pipelines on High Performance Computers (Lecture)

    • 13:00 - 14:00

      Lunch break

    • 14:00 - 16:00

      Generate your own 3D brain model outside TVB (Tutorial)

    • 16:00 - 18:00

      Simulate a Virtual Epileptic Patient (Tutorial)

    March 12, Conference Room 1

    • 09:00 - 10:30

      Parameter optimization in brain model (Lecture)

    • 10:30 - 12:00

      Introduction to birfurcation theory and analyses (Lecture)

    • 12:00 - 13:00

      Visualization of a bifurcation diagram: example with the Jansen-Rit model (Lecture)

    • 13:00 - 14:00

      Lunch break

    • 14:00 - 16:00

      My first bifurcation diagram (Tutorial)

    • 16:00 - 18:00

      Wrap-up and assignments

    Location

    The workshop will be held at the Brain Simulation Section, of the Charité - University Medicine Berlin, which is located at CCM-Luisen-Carreé.


    Registration

    Registration to The Virtual Brain workshop is required for attending the 4 days. Please send an email to Julie Courtiol julie.courtiol@charite.de, and make sure to register early as we only offer limited seats to ensure there are enough tutors for you.

    *Anyone is welcome to register for TVB Node #10!*
    You DO NOT need to be registered as a student at BCCN Berlin in order to participate in this workshop.

    IMPORTANT DETAILS

    HBP Edu. A user account on the HBP Collaboratory platform is required (collab.humanbrainproject.eu). If you do not have an account yet, please request an invitation during your registration to the workshop for creating a (free) HBP Community account, and access to the infrastructure demonstrated during the event.

    Equipment. Please bring your own laptop to work on, and follow the steps below to prepare your software environment.

    Prepare for the workshop

    To get the most out of this workshop as an attendee, you might want to get a head-start by preparing your gear before you arrive:

    1. Download and install the latest stable TVB package,
    2. Test it in its current form to make sure it’s compatible with your computing environment,
    3. Familiarize yourself with the basics by browsing through the included manual (once downloaded TVB, located at /TVB-Distribution/docs/UserManual.pdf),
    4. If you are interested in modifying the code and contributing to TVB, also install the version control system Git.

    In case of any technical problems with TVB installation, please head over to the TVB mailing list.

  • Cologne Neuroscience Day

    6

    Mar

    Cologne, Germany

    THIS EVENT HAS BEEN CANCELLED DUE TO COVID-19.

    Dr. Petra Ritter will deliver a keynote lecture entitled "The Virtual Brain – Multi-scale principles of brain function and dysfunction" at the Cologne Neuroscience Day at Universität zu Köln on March 6th.

    This is the 2nd annual Neuroscience Day event and will also include poster and talk sessions. Dr. Florian Mormann from the University of Bonn will give an additional keynote lecture on "Cognitive adventures of single neurons in the human medial temporal lobe".

    On the event website, you can find the full program and more details. You can sign up via the online registration form.

    Location

    MTI Lecture Hall (Building 44b)
    Lecture Room 1
    Joseph-Stelzmann-Straße 9
    50931 Köln

  • The Virtual Brain at Mobile World Congress Barcelona, 2020

    24

    Feb

    Barcelona, Spain

    We are excited to announce that the The Virtual Brain and Virtual Brain Cloud will have a booth at the Mobile World Congress in Barcelona in February 2020.

    We will be showing our work alongside the Human Brain Project and industry partners Eodyne and Indoc.

    Further details will be announced here, so watch this space!

  • Medical University Charité's 26th Neurokolloquium

    15

    Feb

    Berlin, Germany

    The 26th Neurokolloquium will be held on the 15th of February at the Charité Campus Virchow Klinikum.

    Neurokolloquium is an annual symposium put on by the Charité Clinic and University Outpatient Department for Neurology, during which a variety of lectures and presentations are held on topics from the entire spectrum of work done in the Neurology Department.

    Themes include therapy, diagnosis, historical content and controversial topics from the field. As part of the day's events, Dr. Petra Ritter will present a guest lecture on The Virtual Brain, covering how brain simulations can aid in better understanding and treatment of neurological illnesses.

    Location

    Hörsaal im AUDIMAX
    Campus Virchow-Klinikum
    Augustenburger Platz 1, 13353 Berlin
    (internal: Lehrgebäude Forum 3 / Ecke Weststraße 2)

    A precise map of the lecture hall's location on campus can be found here.

    Full Program and Registration

    Lectures and presentations will be held in German.

    The event is free for employees and students of the Charité Neurology Department.

    The fee for external participants is 20€.

    Please find further details on the program and how to register here.

  • The Virtual Brain at the Human Brain Project Summit

    3

    Feb

    Athens, Greece

    Meet the TVB team at the Human Brain Project Summit & Open Day in Athens from February 3 to 6!

    We will present at the "Explore the Brain" EBRAINS booth on Open day, February 3rd and have a dedicated TVB session on February 5th. Find out about all the TVB tools and services that we made available via EBRAINS!

    HBP is at a crossroads itself, entering its last phase of funding as a FET Flagship project and envisioning its long-term future as a landmark infrastructure in the ESFRI Roadmap. Athens is, thus, a fitting stage for fertile discussions, intense exchange of ideas, and bold new conceptions on the science, infrastructure, research, technology, application, education, and innovation dimensions of neuroscience in general and the Human Brain Project in particular.

    TVB team members in Athens

  • Data Sharing seminar at the BIH

    28

    Jan

    Berlin, Germany

    Please join the Data Sharing seminar at the Berlin Institute of Health on Tuesday January 28.

    Prof. Petra Ritter will be giving a lecture on General Regulations for Processing and Sharing Personal Data.

    The event will be held in German. You can find more details on the BIH event page.

    Full list of speakers

    • Alexander Bartschke, BIH, Medical Information Manager

    • Dr. Evgeny Bobrov, BIH, Referent Open Data und Forschungsdatenmanagement

    • Dr. Peter Brunecker, BIH, stellv. Leiter IT und Co-Sprecher Medical Data Integration Center (MeDIC) (tbc)

    • Dr. Jochen Kruppa, Charité, AG-Leiter Statistische Bioinformatik

    • Prof. Fabian Prasser, BIH, Head of Medical Informatics Group

    • Prof. Petra Ritter, Charité, Direktorin der Sektion Gehirnsimulation

    • Prof. Sylvia Thun, BIH, Director of eHealth and interoperability

    • Dr. Joachim Weber, Charité und BIH, u.a. Oberarzt und CRU-Standortkoordinator

    • Eric Wündisch, BIH, Forschungsplattform Digitale Medizin

    Location

  • Dr. Petra Ritter & Paul Triebkorn present The Virtual Brain at Urania

    21

    Jan

    Berlin, Germany

    Urania Berlin is one of the leading centers of dialog between science, the humanities and the public. We are excited to join the many leading scientists who deliver lectures and talks in their areas of research at Urania.

    Petra Ritter and Paul Triebkorn will present The Virtual Brain at Urania Berlin on January 21st, 2020.

    The talk will be a part of a series called Berlin Brains 2020, during which neuroscientists working in Berlin will present their current work to the public.

    Join us at Urania to hear about how human brains are simulated using The Virtual Brain simulation platform. We will cover how this platform allows researchers to work together, what role the EU Human Brain Project plays and how digital brain simulations help patients.

    Find out more details about the event here.