5^th HBP Student Conference on Interdisciplinary Brain Research

In this workshop we will cover approaches to improve the reproducibility and interoperability of analysis workflows dealing with classical electrophysiological activity data, such as spiking data or local field potentials, from experiment or simulation. In this context, we outline how to combine the e-infrastructure services of EBRAINS with two community-driven tools developed in the framework of the Human Brain Project, Neo and Elephant.

Using interactive material to follow along, we will address

• reading and manipulating electrophysiology data in Python using Neo [1]
• analysis of such data using Elephant [2]
• tracking data analysis pipelines using the HBP Knowledge Graph [3]

[1] https://neo.readthedocs.io
[2] https://elephant.readthedocs.io/
[3] https://kg.ebrains.eu

Workshop Chairs & Tutors:

Workshop Chair:
Michael Denker | Forschungszentrum Jülich

Tutors:
Robin Gutzen, Christiano Köhler, Danylo Ulianych | Forschungszentrum Jülich

Target audience:

Persons interested in handling and analyzing experimental or simulated spike and LFP data.

Pre-requirements for participants:

Beneficial: minimal Python knowledge, minimal knowledge of spike/LFP data

To prepare in advance:

Participants need an EBRAINS account and access to Jupyterlab

EBRAINS is a European research infrastructure for neuroscience which allows scientists to explore data, create models of the brain, simulate and analyze brain behaviour at multiple scales, connect to high performance computing or brain inspired computing technologies, and share data and experiments with the community in an easy and robust way. The goal of this workshop is to help participants define and prototype overarching projects connecting and exploiting different tools and services from EBRAINS. Participants will get a brief introduction to the EBRAINS ecosystem and then be guided through different talks into some highlighted tools for analysis and simulation of brain activity like NEST, Arbor, TVB and L2L. The projects will be performed within interdisciplinary teams to promote networking and create new collaborations.

Workshop Chairs & Tutors:

Chairs: 
Sandra Diaz, Alper Yegenoglu | Forschungszentrum Jülich

Tutors: 
Sandra Diaz, Brent Huisman, Charl Linssen, Michiel van der Vlag, Alper Yegenoglu | Forschungszentrum Jülich

Target audience: 

This workshop targets early carreer scientists from all fields related to neuroscience research. 

To prepare in advance: 

Participants are encouraged to bring their scientific questions, data sets and models.  

Open Science is a continuation of practices which began centuries ago with the advent of academic journal publications. The most recent developments in Open Science is Open Data, recently made possible by new technological capabilities to store large amounts of data, and to access and work on the data over the internet. Leading journals are already now requiring posting of research data in public repositories, to complement the traditional journal article containing the interpretations of the data. Several general data repositories for sharing of research data are available – however, many lack the necessary stewardship and standards for making the research data easy to Find, Access, and Re-use, in accordance with the FAIR guiding principles (Wilkinson et al., Scientific Data 3:160018, 2016). The EBRAINS research infrastructure addresses these challenges by providing tools and services to neuroscientists. The Data Curation service is tailored for integration and sharing of heterogeneous, multimodal neuroscience data, software and computational models. In this workshop you will learn about how (meta)data management and data publication via EBRAINS can contribute to understanding the brain in health and disease, as well as how it can benefit your PhD project and future career. You will also have the opportunity to start the process of creating a data publication on EBRAINS, making sure that your data can be found, accessed and reused by everyone, and - perhaps most importantly - your collaborators and your future self.

Workshop Chairs:

Camilla Blixhavn, Ingrid Reiten, Ulrike Schlögel | University of Oslo

Target audience:

Persons interested in sharing data, software, models, or with interest in open science in general.

More information on this workshop will follow soon.

While powerful technologies such as neurotechnology, computing and Artificial Intelligence can bring many societal benefits, they also raise various ethical concerns including questions about dual use and misuse. The aim of this session is to raise awareness about the topic of dual use, which, understood broadly, means that research and technology can be used for beneficial as well as harmful purposes. This session will draw on the scientific research and practical work undertaken by the HBP Dual Use Working Group which addresses dual use and misuse issues in the HBP and EBRAINS research infrastructure. It will introduce participants to the ways of identifying and addressing dual use research of concern, for example, Responsible Research and Innovation approach which aims to align research and innovation with societal needs. Participants will be encouraged to reflect on their own experiences and potential dual use and misuse issues in their own work.

Workshop Chair:

Inga Ulnicane | De Montfort University
 

Dr.Inga Ulnicane has more than ten years of international and interdisciplinary research, teaching and engagement experience in the field of science, technology and innovation policy and governance. She has published on topics such as international research collaboration, European integration in science and technology and the Grand societal challenges concept as well as undertaken commissioned studies for European Parliament and European Commission. Currently she is a Research Fellow at De Montfort University (Leicester, UK). She is part of the HBP Responsible Research and Innovation work package (WP9). She is Chair of the Human Brain Project’s Dual Use working group. Her current research topics include governance of Artificial Intelligence, dual use and research infrastructures. 

Do you have a vision for your career and know how to realize it? Have you established the right networks to support your career? These questions address several aspects of career development: Especially for early career stage scientists, career development is important and can also be difficult as humans tend to interact with other people who are similar to themselves, thus creating rather homogeneous personal networks. Advancing one’s professional career and / or searching for a new job can be such a problem if networks are too limited.

However, to build a network, individuals must first know their skills, passions and values. If these are clear and reflected, they must be communicated adequately to others so that the person gets known for them. This means that researchers have to build their brand and communicate this brand (consisting of their passions, skills, interests, values) to others.

Structure:

The workshop “Full steam ahead! How to successfully navigate your career journey” at the 5^th HBP Student Conference will explore

• important steps and dimensions of career development (developing and communicating a vision, building networks, keeping a life-domain-balance, etc.)
• tools to implement career goals (e.g. communicating a positive no, using social networks, etc.)
• the benefits of mentoring and sharing experiences with peers
   

Learning outcomes:

Participants of the workshop will

• become familiar with success factors and challenges for scientific and alternative career options.
• gain information on expected formal requirements.
• understand the importance of networks, informal rules and biases.
• learn how to build these networks and deal with the biases.
• reflect your own career goals and build a roadmap on how to get there.
• learn from sharing experiences with your peers.

Workshop Chairs:

Karin Grasenick, Julia Trattnig | convelop, Austria

Target audience:

Early career stage scientists.

In this workshop we discuss some different paths of innovation at universities and research institutions and the relevant stakeholders. After a short theoretical input, we will focus on the discussion of participants' own projects and situations - own start-up ideas or innovation projects results outside or within the framework of the HBP.

Workshop Chair: 

Mario Fallast | Technical University Graz

Since 2006, Mario Fallast's professional career combines two different views on the exciting topic of academic entrepreneurship and the application of research results in business.

Being a founder as well as university member, thus understanding both the academic world as well as the needs and opportunities of start-ups and business world, he is enthusiastic about building bridges between the two worlds to release their full potential.

www.smaXtec.com / www.fth.tugraz.at

www.linkedin.com/in/mariofallast/

Target audience: 

• Persons interested in commercializing their ideas and/or research results
• Persons interested in start-ups and spin-offs

To prepare in advance:

Participants are warmly welcome to bring own cases to the workshop.
A case should include a brief explanation:

• What is the invention / technology about?
• Which problems does it solve?
• Who developed it?
• Are there any steps towards commercialization already planned?

(Summarized in ~1 minute and/or one ppt slide). A case should not include confidential information.

In this workshop, we will present the Fenix infrastructure which is providing compute, cloud and storage resources to neuroscientists, and highlight a number of neuroscience projects that are benefiting from these resources. The participants will then have a chance to use these resources in a hands-on Virtual Machine (VM) tutorial, after which they will be familiar with the process of accessing and launching VMs from a web interface. At the end of the first day of the workshop, participants are encouraged to go away and think about their own research, and how it could benefit from access to computational resources provided by the Fenix infrastructure. A couple of use cases will be presented to the participants to prompt them to think about this.

In the second day of the workshop, the process for applying for resources is explained, followed by a collaborative brainstorming session where participants will bring their ideas about how their research could benefit from access to computational resources. Interactive online survey platforms, such as Survey Monkey or Google forms, will be used to allow participants to identify specific examples of situations where they experienced a need for computational resources to carry out research, or to suggest computationally demanding use cases. These will be discussed in a friendly and collaborative manner, and participants are encouraged to be as imaginative and creative as possible with their suggestions. To end the workshop, there will be an optional hands-on session where participants can then apply for resources for projects coming from their ideas.

Workshop day 1:

• Hands-on VM tutorial (50 mins, AU)
• Coffee/bio break (5mins)
• Overview of the Fenix infrastructure and ICEI resources and examples of projects using resources (15 mins, AN & AU)
• Presentation of two use cases to guide participants to think about creating their own research proposal to use computational resources (20 mins, AG)
  • Participants will be guided through typical computational neuroscience problems that require High Performance Computing resources (e.g. model parameter optimisation, detailed model simulations and large-scale simulations), focusing on two scientific use cases (large-scale simulations of the cerebellar circuit in NEST, and detailed model simulations in NEURON).
• Homework' for participants before Workshop day 2: What research would I do if I had unlimited computational resources? (Online survey)

Workshop day 2:

• Overview of how to apply for resources (15mins, AN)
• Collaborative brainstorming: What research would I do if I had unlimited computational resources (40mins, AG/AN/AU). 
  • After identifying a computationally challenging research project/situation, students will be guided into the design of scientific methodology, goals and implementation plan, choice of software requirements and amount/type of resources for their application.
• Coffee/bio break (5mins)
• Optional hands-on proposal support for interested people (30mins, AG/AN/AU).

Starting from an example of a proposal and their own ideas, participants will draft their own application for computational resources.

Workshop Chairs:

Alex Upton | ETH Zürich
Anne Nahm | Forschungszentrum Jülich
Alice Geminiani | University of Pavia

Target audience:

In this workshop, we encourage participation from young researchers who want to explore how their research can be enhanced by access to the computational resources that they can access from Fenix-ICEI. In particular, researchers who are interested in how they can go beyond their laptop, and start to explore bigger models and simulations.

Pre-requisites for participants:

Basic familiarity with the command line

By taking part in this workshop, participants acknowledge that they agree to the CSCS User Regulations detailed on the following page: https://www.cscs.ch/services/user-regulations/

To prepare in advance:

Participants should install and check that SSH is enabled on their laptops, instructions on how to do this should be sent out to the participants one week in advance (an email will be provided by the workshop organisers that can be sent to them).

Participants learn how The Virtual Brain Cloud (TVB-Cloud) enables neuroscience data integration in the cloud through personalized brain simulation in compliance with the EU General Data Protection Regulations. We will step by step demonstrate the data protection mechanisms implemented in our multi-scale simulation workflows and image processing pipelines comprising e.g. authentication, encryption, sandboxing. We will give an overview of GDPR principles, and discuss prerequisites for lawful processing of individual brain data - that is persoanl health data - and thus falls under particular protection. Examples of data sharing agreements and patient consents as a foundation of lawful personalized brain simulations will be provided. The workshop is participatory. All workflows are available on EBRAINS and can be operated through the Collab.

Workshop Chair & Tutors:

Chair:
Petra Ritter | Charite University Medicine Berlin

Tutors:
Moyez Dharsee | Indoc Research
Lia Domide | Codemart
Paula Papa | Codemart
Michael Schirner | Charite University Medicine Berlin

Target audience:

Scientists interested in Personalized Brain SImulation in the Cloud

Interdisciplinary brain research combines the knowledge of a variety of disciplines, bringing different insights and schools of thought together. Diversity is crucial in brain research as individuals have different brains, shaped by their personal experiences and environments.

To consider diversity in research is in line with the European Commission’s RRI guidelines and the gender agenda for Horizon 2020. The HBP aims to play a pioneering role in promoting awareness and advancing how gender and diversity are considered in research and innovation. Examples from the field of AI and Machine Learning illustrate that diversity in research is also a key factor in technical innovations and developments. As this technology is designed by humans, it may be encoded with the biases of its developers or fed with prejudiced or biased data.

Sex and gender might intersect with other diversity traits, such as age, race, social background or culture. Additionally, research findings might have different implications for different user groups or stakeholders (e.g. different treatments for women, pregnant women and men or for children and adults, showing that diversity traits as sex and age might intersect).

Structure:

The workshop “Which brain are we looking at? About the role of diversity in brain research” at the 5th HBP Student Conference will explore

• topics and definitions of terms and concepts like diversity, sex, gender and intersectionality
• examples of diversity in brain research
• the role of a diverse research team

Learning outcomes:

Participants of the workshop will

• learn to reflect their own research situation (content and team) regarding aspects of diversity
• get practical tools to implement diversity in their everyday work
• develop further examples for diversity in brain research, taken from their own research experience

Workshop Chairs:

Karin Grasenick, Julia Trattnig | convelop
 

Target audience:

If participants are interested to get feedback, they are welcome to bring examples for diversity from their own research.

To prepare in advance:

If participants are interested to get feedback, they are welcome to bring examples for diversity from their own research.

Registration is mandatory and is open until 14 January 2021.
Attendance is open to anyone and free of charge.
 

A: I already have an EBRAINS account.

1. Click on the “Register” Button
    
2. Log in to your EBRAINS account
    
3. Enter your availabilities and accept the GDPR Statement.
    
4. Click on “Please provide additional info by filling out this form (person and meeting related questions)” and enter the requested details.
    
5. Once you have completed all fields and clicked on “Update”, you will receive a registration confirmation via e-mail. (Please note that you will receive a confirmation e-mail only for the first time you have entered all details. In case you update your registration details, no additional e-mail will be sent).

B: I do not yet have an EBRAINS account.

1. Please go to https://ebrains.eu/register and create your account free of charge. As the EBRAINS Access Policy requires that users identify themselves by means of an institutional email address, please make sure to register with your institutional e-mail address.
    
   • All new users with a personal institutional e-mail address from a pre-identified institution will be provided an expedited registration process.
      
   • If your institution is not yet on the list of pre-identified institutions, please contact the EBRAINS support team from your institutional e-mail address and it will be added promptly.
      
   • If you cannot register with an institutional e-mail address or experience any other problems, please contact us at education@humanbrainproject.eu.
      
2. Once you have received your EBRAINS account please follow the steps from option A.

The conference starts on Monday 1 February and lasts until Thursday 4 February 2021. It will be a virtual conference and the programme will comprise keynote lectures, student sessions, poster sessions as well as social events.

A more detailed schedule will be published here on this webpage during autumn 2020.

Please note that the abstract submission is already closed. If you have submitted your abstract and are now preparing the final version, please make sure to align with the guidelines below.

Authorship

Please accurately include all co-authors and their affiliations. If in doubt whether a person’s contributions should or should not be considered as authorship, please refer to 
http://www.icmje.org/icmje-recommendations.pdf.

Abstracts

Abstracts must be in a Word document format. The abstract word and character limits are as follows:

• Title: 500 characters
• Text: 1,000 words
• Number of Figures: 2
• No Supplementary Material

Abstracts that should be included in the proceedings, must be organised according to the IMRaD format [Introduction/Motivation, Methods, Results and Discussion], with several sentences addressing each of these elements. Please find a template for your convenience.

References should be included at the end of the abstract. Please note that the word count includes captions but not references. It is allowed to add acknowledgements to the abstract.

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.

If you have any questions about the abstract submission or the conference, please contact us at education@humanbrainproject.eu.