6th HBP Student Conference on Interdisciplinary Brain Research

 

22–25 February 2022
Virtual Event

Download the Preliminary Scientific Programme 4.2 MB

 

 




FAQ's and all you need to know
 

Registration for virtual participation

  • Admission to scientific sessions available for virtual participation
  • Admission to workshops available for virtual participation
  • Conference material

Lately, we have received information about emails from third party service providers that ask speakers or participants of the conference to confirm their hotel reservation. Please note that we do not offer such services or maintain any collaborations with such service providers. Any communication in regards to the conference will be sent to you by education@humanbrainproject.eu

 

The conference will start on Tuesday 22 February 2022 at 2:00 PM CET and will end in the afternoon of Friday 25 February 2022. The programme comprises keynote lectures, student sessions, poster sessions, workshops as well as social events.

 

Registration fee waivers are available for a limited number of participants in financial need that want to partake in the conference.

To apply for a fee waiver, please send an email to education@humanbrainproject.eu with a short explanation (max. 200 words).

 

The link to our virtual conference platform as well as the online credentials will be sent out to all registered participants a few days prior to the conference.

 

To make this virtual conference an interactive experience, it is important that you have access to a stable internet connection, good audio (with microphone) and ideally (not mandatory) a webcam for video communication.

Also, to have the full conference experience it is important that you have installed the Zoom Desktop Client application (v5.7.0 or higher) and that you access the conference platform via the latest version of Google Chrome

 


 

Workshop descriptions

​​​​​​​Back to Programme overview

 

Wednesday, 23 February 2022 (10:00 – 11:30 CET)
 

 

Abstract

Join the EBRAINS Community Workshop for a discussion on interdisciplinary collaborations, what barriers to overcome and find opportunities for collaboration with other workshop participants. The workshop will include group discussions and work on specific cases. 

 

Workshop Speaker

Mr. Lars Klüver, MSc. Environmental Biology/Ecology, is Director of the Danish Board of Technology and has a status as international expert in technology assessment and foresight methodology, with special emphasis on practices engaging stakeholders, policy-makers and citizens. He has been scientific advisor on a multitude of national and international research, foresight and technology assessment activities, and has himself led projects in fields as e.g., biotechnologies, energy and climate, ICT, health, agriculture and environment, besides numerous methodological projects.

The Danish Board of Technology is a not-for-profit corporate foundation working for the common good. The mission of the DBT is to work for society’s development being shaped by informed and forward-looking collaboration between citizens, experts, stakeholders, and decision-makers.

 

Workshop Chairs

Sara Christina Martinez, Aske Palsberg, Natalie Roosta | Danish Board of Technology

 

Target audience

  • We welcome all interested participants but will be targeting early career researchers who are looking to either establish project collaborations, network or understanding of researchers with another background than themselves.
     
  • We welcome participants with specific ideas or projects where they are looking for partners and collaborators within another discipline than their own, but cases will also be developed for the workshop, so this is not a requirement.  

 

Expected learning outcomes

  • Introduction to the EBRAINS Community
  • Insight into benefits and challenges in interdisciplinary collaborations
  • Networking and opportunity to find project partners or other forms of collaborations
  • Knowledge sharing  

 

Preparations:

Before the workshop it will be beneficial for the participants to consider:

  • Where do you often meet, interact, or collaborate with individuals or groups within another discipline than their own?
     
  • Which barriers do you experience from interdisciplinary collaborations and interactions? How have you tried to overcome these barriers?
     
  • Which benefits do you experience from interdisciplinary collaborations and interactions?
     
  • Participants should also read the cases that will be send out to participants prior to the workshop and decide which case to work with during the workshop.
     
  • Participants are welcome to bring their own case to work with during the workshop – in that case the workshop chairs should receive the case description 1 month prior to the workshop. More instructions will be prepared and sent out.
     
  • The EBRAINS Community website will be used – all participants are therefore encouraged to sign-up for the EBRAINS Communiny and create a profile, prior to the workshop.  

 

Maximum number of participants:

20-30 people, depending on COVID19-related room capacity

 

 

 

Abstract

Arbor is a performance portable library designed to handle very large and computationally intensive simulations of networks of multi-compartment neurons. At the same time, Arbor is designed to be easy to use and understand, so that also beginners to computational neuroscience can get up to speed quickly. Furthermore, Arbor aims to prepare computational neuroscientists to take advantage of HPC architectures. Whether your model is large or small, Arbor is able to optimize and compute your result on almost any current and future hardware.

In this session, we’ll first introduce the Arbor simulator library. We will go into questions such as:

  • What is portability and why is it relevant to a computational neuroscientist?
  • What is performance portability and why is it relevant to a computational neuroscientist?
  • How did the above considerations impact Arbors design?
  • How did it impact Arbors API design, which is to say: how easy to use is all this?
  • What’s new in Arbor? Current developments include performance improvements for gap junctions, file format compatibility, the Arbor GUI and more!

After the introduction, it is time for a hands-on session where Arbor is used to:

  • construct a morphological cell
  • construct a network
  • configure how the simulation is run (single core, multi core, GPU, or MPI, up to you!)
  • produce results! 

 

Workshop Speaker

Hi, I’m Brent F.B. Huisman, and I’ll be showing you how to build a small ring network in Arbor in the 6th HBP Students workshop.

Right now I work in the Arbor team. Arbor is neuro-scientific simulator of networks of morphologically detailed cells, suited for distributed simulation on supercomputers. Before this, I worked as a postdoc in radiotherapy, where I used Monte Carlo tools to estimate the in-vivo dose to every patient based on logged data, and I defended a doctoral thesis on the subject of prompt gammas for treatment verification in particle therapy. Here I developed and validated a variance reduction technique, which was implemented in Gate. I’ve got a master’s degree in particle physics, and I defended a thesis on proton computed tomography.

As a member of various boards and student organisations, I’ve learned what makes a good team, and what we can accomplish united. I’ve had trainings on leadership and coaching, and have had the opportunity to apply these skills in practice. I’ve thoroughly enjoyed my time as treasurer, as secretary of an event with the top strategy consultants of the world and co-organizing a symposium featuring a Nobel prize winner.

 

Workshop Chairs

Brent F.B. Huisman | Forschhungszentrum Jülich

 

Target audience

  • Any neuroscientist (in training) looking to get into computational neuroscience, or interested in new tools.
     
  • Participating in the tutorial assumes that attendees are comfortable using the Python programming language. No prior knowledge of Arbor or constructing neuroscientific simulations is required.

 

Expected learning outcomes

The following questions will be covered:

  • What is portability and why is it relevant to a computational neuroscientist?
  • What is performance portability and why is it relevant to a computational neuroscientist?
  • How did the above considerations impact Arbors design?
  • How did it impact Arbors API design, which is to say: how easy to use is all this?
  • What’s new in Arbor? Current developments include performance improvements for gap junctions, file format compatibility, the Arbor GUI and more!

 

Preperations:


Although preparation is not required, having a look throughthe Arbor documentation beforehand can help you get the most out of this tutorial. If you wish to run the tutorial on your own machine, make sure you have Python installed (v3.6 or higher) and have installed the `arbor` and `seaborn` packages through `pip`, e.g. `pip install arbor seaborn`.

Note: Windows users are supported through WSL and WSL only at this time.

Main website: arbor-sim.org
Documentation: docs.arbor-sim.org
Tutorials: docs.arbor-sim.org/en/stable/tutorial

 

Maximum number of participants:

30 people

 

 

Abstract

EBRAINS is a European research infrastructure for neuroscience that allows scientists to explore data, create models of the brain, simulate and analyse brain behaviour at multiple scales. Thereby emerging computational limitations are addressed by enabling access to high-performance computing or brain-inspired computing technologies. All results, as well as experimental data, can be shared with the community in an easy and robust way following FAIR principles. 

This workshop will provide a quick overview of the different tools and services available in EBRAINS. It will address, in an interactive way, how to use EBRAINS for specific use cases from the participants and focus on exploring all the potential that EBRAINS, as a digital research infrastructure, provides to its users. Researchers will have the opportunity to get creative and combine the different EBRAINS components to respond to existing questions and formulate new avenues based on collaboration, sharing, co-design, and innovation.

 

Workshop Speaker

Claudia Bachmann, Marissa Diaz | Forschungszentrum Jülich 

Pictures & Bios to follow soon.

 

Workshop Chair

Claudia Bachmann | Forschungszentrum Jülich

 

Target audience

Young Researchers that are new in EBRAINS, Established EBRAINS users who would like to get inspiration for broadening their research scope.

 

Expected learning outcomes

Minimum: On overview of what services/tools are offered by EBRAINS.
Maximum: What are the concrete tools /services that I can use for my research and where do I find more information about them.

 

Preparations:

No preparation is needed. But! this workshop would be a good opportunity to easily figure out what kind of services/tools in EBRAINS would suit your research. So, if you send me your research ideas in advance, I will pick up on them during the session and give a short introduction to the tools you could use to address them.

 

Maximum number of participants:

20

 

 

 

Abstract

Extracting useful information from experimental and simulated data is not a straightforward endeavour. The easy representation of models and their interaction with data sources and other simulation and analysis tools is also becoming essential to gain new knowledge and leverage the emerging software infrastructure to study the brain.

We will introduce different visualization tools which can be used to interactively create, explore and analyse experimental and simulated data, extracting useful information. These tools span along different spatial and temporal scales which describe the function of the brain.

We will then demonstrate a use case where modeling, simulation and visualization come together around a specific scientific question.

Finally, we will engage with the attendees in order to know more about their specific scientific projects, about how their interests are covered by the use case shown, and also to help them identify the right set of tools from the EBRAINS infrastructure to visualize and interact with data, models and simulations.

Keywords: Visualization, cosimulation, modelling 

 

Workshop Speakers

Óscar David Robles Sánchez, Susana Mata Fernández | VG-Lab, Universidad Rey Juan Carlos, Spain
Sandra Diaz | Forschungszentrum Jülich

Pictures and bios to follow.

 

Workshop Chair

Óscar David Robles Sánchez | VG-Lab, Universidad Rey Juan Carlos, Spain

 

Target audience

All researchers and students who would like to work with experimental and simulated data with the need of analysing their results. Also all ones interested in visualization and modeling tools for this kind of data.

 

Expected learning outcomes

The participants will learn about some of the available visualization and modeling tools available in EBRAINS and will have the opportunity to interact with experts and get guidance around the infrastructure tools in order to fit their own specific use cases and scientific goals

 

Preparations:

none

 

Maximum number of participants:

40-50 people

 

 

 

Abstract

Data-driven modelling of the brain requires a neuroinformatic framework implementing a general strategy to accommodate experimental data at different scales. To this end, we have developed the Brain Scaffold Builder (BSB), a tool for structural and functional microcircuit modelling. The BSB provides an organized staged workflow, multiple strategies for cell placement and connectivity, a configuration system capable of including detailed neuronal and synaptic models and the support for multiple simulators with transparent parallel processing. It is provided as an open-source package, applicable for multi-scale modelling of different brain areas. The interfaces with several simulators (NEURON, NEST, Arbor) allow to investigate the same brain region at different levels of resolution, depending on the scientific question about structure-function relationships. BSB effectiveness was tested on the cerebellar network, which has a complex geometry and raises a broad set of modelling challenges. Therefore, the first detailed computational model of the entire cerebellar cortical microcircuit, including both the granular and molecular layer, was generated, so unveiling the structure-function-dynamics relationship of the circuit.

 

Workshop Speakers

Claudia Casellato got her PhD in Bioengineering at Politecnico di Milano in 2011. Then, she was a research fellow at Politecnico, on neuroengineering, neurorobotics and rehabilitation in motor learning. From 2017 she is Assistant Professor at Dept. of Brain and Behavioral Sciences of University of Pavia, coordinating the neurocomputation lab. Within the EU Human Brain Project, she works in developing and applying computational multi-scale neural models mainly reconstructing the cerebellar circuit, to implicitly generate high-level functions from elementary neural features and microcircuit mechanisms, in physio and pathological states. She has more than 35 publications on international peer-reviewed journals.

 

Alice Geminiani obtained the Master’s Degree in Biomedical Engineering cum laude in April 2015, and the PhD in Bioengineering cum laude in July 2019, at Politecnico di Milano, working in the field of computational neuroescience. During the PhD, she has developed multiscale models of the cerebellar circuit using Spiking Neural Networks, to investigate cerebellar functioning and pathologies, specifically studying the role of complex single neuron dynamics and long-term plasticity in cerebellum-driven motor learning. The research activity has been carried out within CerebNEST, Partnering Project of the Human Brain Project, between the NEARLab of Politecnico di Milano and the University of Pavia. She has spent periods abroad as a visiting student at the University of Granada – CITIC, during the Master thesis, and the Erasmus Medical Center – Department of Neuroscience, during the PhD. She is currently a PostDoc researcher at the University of Pavia in Egidio D’Angelo’s laboratory, working on the reconstruction of a full-scale mouse cerebellar model mapped on the Allen Brain Atlas, within the Human Brain Project Voucher Virtual Mouse CerebNEST. She has experience in neuron model development and simulations in NEST.

 

Robin De Schepper is a PhD student in Computational Neuroscience at the University of Pavia. He graduated in Molecular and Cellular Neuroscience magna cum laude from the University of Antwerp. His master thesis expanded the Tsodyks-Markram model for short-term synaptic plasticity to explain previously uncaptured supralinear facilitation. He followed an internship at the Receptor Biology Lab of prof. dr. Stuart Maudsley where he developed Pyxis, a pipeline that mines the academic text body for data to compare signatures of GPCR ligands to disease signatures. He is interested in open access and distributing open source software that benefits the neuroscience community

 

Workshop Chair

Claudia Casellato | University of Pavia

 

Target audience

Master students, PhD students, early career researchers, with basic knowledge on Python programming and computational neuroscience principles

 

Expected learning outcomes

Participants will learn to manage a flexible framework to reconstruct and simulate a brain network, reconfigure some elements of the network (interchangeable components). 

 

Preparations:

pip install bsb”  https://bsb.readthedocs.io/en/latest/usage/installation.html

 

Maximum number of participants:

none

 

 

 

Thursday, 24 February 2022 (10:00 – 11:30 CET)
 

 

Abstract

This workshop teaches you how to exploit the thundering success of deep learning within the domain of computational neuroscience. You will learn about Norse, a bio-inspired extension of the massively successful deep learning library PyTorch. Norse adds neuron primitives, plasticity, and learning algorithms to the PyTorch infrastructure, which brings three benefits we will highlight in the workshop:

  1. rapid modelling and execution of experiments within minutes
     
  2. unrestricted combinations of biological and artificial neural network primitives and learning rules
     
  3. translation of network models to high-performance computing clusters and neuromorphic hardware.
     

Finally, the workshop provides a brief exposition on useful community-based tools to increase your productivity. 

 

Workshop Speaker

Christian G-Pehle is a postdoc in physics at the Kirchoff institute of physics at the University of Heidelberg. He is a co-author of the spiking neural network library, Norse, and pioneered the EventProp optimization algorithm for spiking neural networks.

 

 

Workshop Chair

Jens E. Pedersen | KTH Royal Institute of Technology

 

Target audience

Computational neuroscientists, computer scientists, data scientists

 

Expected learning outcomes

Using Norse, participants will learn to 1) simulate and optimize bio-inspired spiking neural networks, 2) combine learning principles from artificial and spiking neural networks, and 3) use the network accelerator PyTorch Lightning to increase productivity and training speed.

 

Preparations:

Participants only need a computer with internet access. Experience with Python is an advantage, but not a requirement.

 

Maximum number of participants:

none

 

 

 

Abstract

Results of brain research, like those of any impactful research, can be used for socially beneficial as well as harmful purposes; namely, it is inherently dual use research of concern. Issues of dual use of concern, misuse and unintended use are widely recognized as the critical socio-technical issues that need to be addressed to ensure responsible development of brain research. In the Human Brain Project (HBP), we have developed a novel approach to address dual use of concern and misuse in neurotechnology. This approach goes beyond the traditional civil-military dichotomy understanding of dual use and considers broader political, security, intelligence and military uses of concern. A range of activities has been launched to continuously identify and discuss any potential concerns and misuse issues, to create networks of responsibility and ‘safe spaces’ to reflect on potential concerns and ways of addressing them. To sum up, doing brain research for good involves not only assuming and taking for granted its benefits and intended uses but also continuous reflection on any potential concerns, misuses and unintended uses, and ways to address them.

 

Workshop Speakers

Dr. Inga Ulnicane has more than 15 years of international and interdisciplinary experience of research, teaching and engagement in the field of science, technology and innovation governance, policy, and politics. She has published on topics such as governance and policy of Artificial Intelligence, dual use, international research collaboration, European integration in research, and Grand societal challenges. In addition to academic publications, she has prepared commissioned reports for the European Parliament and European Commission. Currently she is Senior Research Fellow at De Montfort University, Leicester, UK, and chairs the Human Brain Project’s Dual Use Working Group.  

 

Manuel Guerrero | Uppsala University

Image and bio to follow soon.

 

Workshop Chair

Inga Ulnicane | De Montfort University

 

Target audience

Everyone interested in societal and ethical aspects of brain research is welcome. No pre-required knowledge is expected.

 

Expected learning outcomes

Participants will gain understanding of dual use of concern and misuse in brain research (including AI, robotics and computing), and learn about the ways to identify and address potential concerns and misuse issues. They will learn about approaches such as Responsible Research and Innovation and the AREA framework of anticipation, reflection, engagement and action.

 

Preparations:

No need to prepare in advance. If interested, please have a look at our webpage https://www.humanbrainproject.eu/en/social-ethical-reflective/about/dual-use/

 

Maximum number of participants:

none

 

 

 

Abstract

Do you know how to navigate within and across different university structures, which procedures and scientific practices are relevant for your career? Have you established the right networks to support your career? Do you know how to become part of core communities? Do you want to contribute to an inclusive working environment and build your own reflective leadership skills?


These questions are addressed in the workshop offering insights in rules and practices of academic systems and hands on tools for you career. Your own experiences and questions will contribute to an open dialogue on success of your career aspirations – as part of or leader of inspiring and inclusive teams. 

 

Workshop Speaker

Karin Grasenick (convelop cooperative knowledge design gmbh) graduated in Computer Science and Biomedical Engineering. Her thesis on innovative non-invasive techniques to measure stroke volume led to a growing interest in inter- and transdisciplinary research, diversity in research content and equal opportunities in science. She lectures, coaches and supports teams, universities and international projects in diversity and change management. In HBP, she actively supports the recognition of diversity as a success factor for research and innovation. Together with her team she provides tools and techniques for researchers accordingly. 

 

 

Julia Trattnig (convelop cooperative knowledge design gmbh)

 

Bio to follow soon.

 

 

Workshop Chairs

Karin Grasenick, Julia Trattnig | convelop cooperative knowledge design gmbh

 

Target audience

PhD and Postdocs, EBRAINS internal and external users

 

Expected learning outcomes

  • Understanding science as academic system
  • Navigating in and across universities
  • Learning how to build networks across hierarchies, professions, and further diversity traits
  • Self-empowerment and inclusive leadership in scientific systems
  • Learning from sharing experiences with peers

 

Preparations:

none

 

Maximum number of participants:

20-30 (depending on COVID-19 related room capacity)

 

 

 

Further information will follow soon.

CONFERENCE CHAIRS

Alice Geminiani | University of Pavia
Tabea Kirchner | Forschungszentrum Jülich
Paschal Ochang | De Montfort University


PROGRAMME COMMITTEE

Joana Covelo | August Pi i Sunyer Biomedical Research Institute 
Sandra Diaz | Forschungszentrum Jülich
Carmen Lupascu | Italian National Research Council
Taylan Özden | Technical University Darmstadt
Jens Egholm Pedersen | KTH Royal Institute of Technology
Ingrid Reiten | University of Oslo
Alper Yegenoglu | Forschungszentrum Jülich

 

ORGANISER

HBP Education Programme | Medical University Innsbruck
 

CONTACT

education@humanbrainproject.eu