LAB VISITS

 

HBP Lab visits

 

The HBP Education Programme is collecting information on lab visits offered by HBP partners. A list of contacts can be found below. Please note that applications have to be sent directly to the respective lab.

Lab visits are a possibility for applicants to develop new technical or conceptual expertise for implementation in their research as well as their home institute's research programme. The target group are early career researchers who:

  • Work for an HBP Partner Institution and want to visit an HBP laboratory other than their own
  • Do not work for an HBP Partner Institution and want to visit an HBP Partner laboratory

 

If you are interested in offering lab visits, please fill out the HBP  Lab Visit opportunities form  and send it to education@humanbrainproject.eu.

 

HBP LABS DIRECTORY

Do you want to gain practical experience and learn new scientific methods? Have a look at our directory of lab visits offered by HBP partners: 
 

APE Lab (Parallel Computing Lab – Computational Neuroscience)

Istituto Nazionale di Fisica Nucleare (INFN), Rome, Italy

 

Lab visit description

During this lab visit, you will 

(a) get familiar with the tools and methods developed by the APE Lab concerning:

1. simulations and models of spiking neural networks 
2. analysis of experimental data (ECoG, Ca-imaging, EEG) and of simulation outcome  

(b) validate and improve tools and methods, evaluate possible extensions and/or further application scopes, promote collaborations.

 

Scientific methods offered to the student

  • DPSNN, the simulation engine developed by the APE LAB for distributed and plastic spiking neural network simulations
  • Expertise with the NEST simulator (for the simulation of deep sleep and awake states)
  • SWAP, the analysis pipeline developed by the APE LAB for the study of slow wave activity in deep sleep and anaesthesia states (Matlab, Python) using multi-electrode-array data and imaging data
  • Inference methods for the prediction of cortical connectivity and data-constrained simulations
  • Thalamo-cortical models of sleep-memory interactions
  • Likelihood-based learning models in spiking neural networks

 

Duration of lab visit

up to 4 weeks

Period

April 2020-April 2023 (excluding months December, July, August)

Costs covered by lab

Research material, access to HPC systems, office space; work insurance;
further coverage could be evaluated case by case

Costs to be covered by participants

Travel costs, accommodation, living expenses;
financial support can be offered, evaluated case by case

Required language skills

English

 

Application details

Application deadline: Reasonable notice (at least 1 week) with respect to the start date of the visit

Please include the following information in your application:

  • Name, degree
  • Name and contact details of current supervisor
  • CV
  • List of publications
  • Short motivation letter for the lab visit, with description of current research topic and research interests
  • Recommendation letter by supervisor/mentor, including why the lab visit is beneficial for the applicant
  • Copy of passport
  • Copy of highest university degree
     

Applications will be evaluated as received. The decision will be based on the information provided by the student; further action (as contacting the supervisor and/or requesting a Skype interview to assess interests and motivation) could be evaluated case by case.

Application to be sent via email to: 

Pier Paolucci 

pier.paolucci@roma1.infn.it, CC to Giula De Bonis giulia.debonis@roma1.infn.it

Subject Line: “HBP Lab Visits at APE Lab”

Computational Neuroscience Laboratory, Institute of Biophysics

CNR, Italy

 

Lab visit description

Hands-on activities related to the HBP Brain Simulation Platform and cellular level model of the hippocampus.

 

Scientific methods offered to the student

  • Computational neuroscience methods for cellular level modelling (NEURON, python)
  • Tools and implementation strategies used within the HBP Brain Simulation Platform

 

Duration of lab visit Up to 2 weeks
Costs covered by lab Research material, access to HPC systems, office space
Costs to be covered by participants Travel costs, accommodation, living expenses
Required language skills English

 

Application details

Please include the following information in your application:

  • Name of current supervisor
  • CV
  • List of publications
  • Copy of passport
  • Recommendation letter by supervisor/mentor
  • Short motivation letter for choosing the lab
  • Statement of funding availability for travel and subsistence costs during the visit

 

Applications will be evaluated as soon as they are received. The decision will be based on the information provided by the student, the requested period for the visit, and the number of concurrent visits, which cannot be more than 5 at the same time.

 

Application to be sent via email to:

Michele Migliore

michele.migliore@cnr.it, CC to Alessia Bonafede alessia.bonafede@pa.ibf.cnr.it

Department of Cognitive and Systems Neuroscience, SILS

University of Amsterdam, Netherlands

 

Lab visit description

The visitor will get experience in one or more of the methods below and will collaborate with HBP on one of the following tasks:

  1. neurophysiology of multisensory integration, episodic memory and object recognition in rodents;
  2. generative models of cortical networks;
  3. decoding of scene information in conscious and unconscious states or
  4. data analysis, curation, and computing with recurrent networks. Our team will support the visitor with guidance throughout the techniques.

 

Scientific methods offered to the student (any or a combination of the following)

  • Rodent behavioural training 
  • In vivo chronic electrophysiological recordings
  • Optogenetics
  • 2-photon calcium imaging
  • Computational modelling
  • Advanced data analysis

 

Duration of lab visit

6 months

Period

September 2020 to February 2021/ September 2021 to February 2022

Costs covered by lab

Research material, basic facilities (internet, desk, participation to experiments and modelling), supervision                                            

Costs to be covered by participants

Travel costs and accommodation must be covered by the visiting student or the institution of origin.

Required language skills

English

 


Application details

Please include the following information in your application:

  • Name of the applicant
  • Name of institution of origin
  • Name of current supervisor
  • Publication list
  • CV, diploma and motivation letter (in one PDF)
  • 2 recommendation letters
  • Grades list, courses and transcript
  • Copy of passport
     

Applications will be evaluated as soon as they are received. The decision will be based on information provided by the student, the lab's research plan, and the number of other applicants. Administrative prearrangements prior to visit may take up to two months.
 

Application to be sent via email to: Cyriel M.A. Pennartz and Conrado Bosman Vitti

FZI Research Center for Information Technology 

Karlsruhe Institute of Technology, Germany

 

Lab visit description

Hands-on activities related to the HBP Neurorobotics Platform and spiking closed loop motor control of robots.

 

Scientific methods offered to the student
 

  • Tools and implementation strategies used within the HBP Neurorobotics Platform
     
  • Simulation of neuronal models in Nest and Nengo
     
  • Machine learning
     
  • Python programming

 

Duration of lab visit 1 week – 3 months
Costs covered by lab Research material, use of robots and lab material, office space
Costs to be covered by participants Travel costs, accommodation, living expenses, insurance
Required language skills English 

 

Application details


Please include the following information in your application:

  • Current (HBP) research group, supervisor and activities within HBP
  • Short description of programming experience
  • Letter of motivation
  • List of publications
  • CV
     

Applications will be evaluated as soon as they are received. The decision will be based on the information provided by the student, the requested period for the visit, and the number of other applicants.

 

Application to be sent via email to:

Arne Rönnau

roennau@fzi.de

Institute for Neuroscience and Medicine: Structural and functional organisation of the brain (INM-1)

Forschungszentrum Jülich, Germany

 

Lab visit description

The INM-1 focuses on the development of a three-dimensional model of the human brain based on cyto- and receptor architectonic, genetic and functional data as well as on information regarding connectivity between different brain regions. For further information visit the lab website:

http://www.fz-juelich.de/inm/inm-1/EN/Home/home_node.html;jsessionid=3C8FD0E0E794F4531D8D7F95A5D61E76

 

Scientific methods offered to the student

  • Lab visit – brain slicing, staining, labelling (receptor autoradiography) etc. (duration: 2 weeks)
  • Cytoarchitectonic mapping (duration: 3 months)
  • Polarized light imaging (duration: 3 months)
  • Receptor architectonic mapping (duration: 4 months)
     
Duration of lab visit 2 weeks – 4 months (depending on topic)
Costs covered by lab Lab material 
Costs to be covered by participants Travel costs, accommodation
Required language skills English; German beneficial but not mandatory

 

Application details

Please include the following information in your application:

  • Name, degree
  • Description of current research topic and motivation for the lab visit
  • Name of the current supervisor
  • Short statement by supervisor why lab visit is beneficial for the applicant
  • CV
  • Copy of highest university degree
  • Copy of passport

 

Application to be sent via email to:

Sabine Bradler

s.bradler@fz-juelich.de

Institute for Neuroscience and Medicine: Computational and Systems Neuroscience (INM-6 / IAS-6)

Forschungszentrum Jülich, Germany

 

Lab visit description

Techniques to record neuronal data from single neurons and population of neurons are rapidly improving. Meanwhile, recordings are possible from hundreds of channels simultaneously while animals perform complex tasks. Thus also the analysis of such data becomes increasingly challenging. In addition, progress in simulation technology and computer hardware enable the simulation of full-scale models to interpret such data. The lab visit aims at providing deeper insights in state-of-the-art analysis or simulation approaches. The course is addressed to excellent master and PhD students and young researchers who are interested in learning advanced techniques in data analytics and simulation and in getting hands-on experience in computational neuroscience.

Experienced researchers will help the visitor to learn how to operate one of two complex software packages of the HBP efficiently and safely. Participants will analyse provided data on their own using the tool box Elephant or will learn how to carry out neuronal network simulation with NEST.

 

Scientific methods offered to participants

  • Neuronal network simulations with NEST. NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. The student can also learn to extend the simulator according to need.
     
  • Analysis of electrophysiological data with Elephant. Elephant is an open-source Python library that provides tools for the analysis of neuronal activity data, such as spike trains, local field potentials and intracellular data. Elephant focuses on generic tools that characterize the coordinated dynamics of large neural populations and methods that analyse the relationship of data recorded on multiple scales of observation. The student can also learn to extend the toolbox to need.

 

Duration of lab visit 3 days
Costs covered by lab All material and computing time
Costs to be covered by participants Travel costs, accommodation
Required language skills English

 

Application details

Please include the following information in your application:

  • Short description of programming experience
  • CV
  • Letter of motivation

 

Applications are reviewed every 2 months and participants are selected according to qualification and success likelihood.

 

Application to be sent via email to:

Anne Elfgen

a.elfgen@fz-juelich.de

Institute for Neuroscience and Medicine: Brain and Behaviour (INM-7)

Forschungszentrum Jülich, Germany

 

Lab visit description

The goal of the INM-7 is to obtain a more detailed characterisation of the organisation of the human brain and its inter-individual variability in order to better understand its changes in advanced age as well as neurological and psychiatric disorders. Based on this knowledge, new approaches for diagnosis and outcome prediction at the level of individual patients are developed. We pursue this objective by combining multi-modal MR imaging, detailed neuropsychological characterisation and innovative methods of data analysis and simulation. An important focus of the institute is to provide the developed tools and results to the scientific public in the form of software and data sets enabling the broad use of our research.

Further information: https://www.fz-juelich.de/inm/inm-7/EN/Home/home_node.html;jsessionid=ED412D114CF5DDC7E15AF66799AEEE34

 

Scientific methods offered to the student (minimum stay 1-2 months)

  • Neuroimaging analytics and brain-behaviour relationships
  • Meta-analytics and data-base driven modelling of brain activation patterns
  • Clinical neuroimaging and individual prediction of clinical states
  • Simulation and modelling of brain dynamics

 

Duration of lab visit Duration at least 1-2 months (depending on topic)
Costs covered by lab Lab material, computational resources
Costs to be covered by participants Travel costs, accommodation
Required language skills English; German beneficial but not mandatory

 

Application details

Please include the following information in your application:

  • Name, degree
  • Description of current research topic and motivation for the lab visit
  • Name of the current supervisor
  • Short statement by supervisor why lab visit is beneficial for the applicant
  • CV
  • Copy of highest university degree
  • Copy of passport

 

Application to be sent via email to:

Simon Eickhoff

S.Eickhoff@fz-juelich.de

Laboratory for Neuro- and Psychophysiology

KU Leuven, Belgium

 

Lab visit description

Observation of experiments
 

Scientific methods offered to the student

  • MRI in nonhuman primates
  • Behavioural experiments in nonhuman primates
  • Electrophysiology in nonhuman primates
  • Electrical microstimulation and optogenetics in nonhuman primates

 

Duration of lab visit 2-3 days
Costs covered by lab Research material
Costs to be covered by participants Travel costs, accommodation
Required language skills English

 

Application details

Please include the following information in your application:

  • Name of current supervisor
  • CV
  • Skills list
  • Recommendation letter
  • Copy of passport
  • Recent TB test (< 6 months old, needs to be negative)

 

Application to be sent via email to:

Wim Vanduffel

wim.vanduffel@kuleuven.be

Parietal team, Inria-CEA 

Saclay, France

 

Scientific methods offered to the student

  • Human brain imaging
  • Data analysis
  • Statistics
  • Machine learning
  • Python programming

 

Duration of lab visit 1 week – 2 months
Costs covered by lab Company restaurant 
Costs to be covered by participants Travel costs, accommodation; students should bring their own laptops
Required language skills  

 

Application details


Please include the following information in your application:

  • Letter of motivation
  • CV

 

For long stays, the administrative application may take 2 to 3 months.

 

Application to be sent via email to:

Bertrand Thirion

bertrand.thirion@inria.fr

PRECISE – Platform for Single Cell Genomics and Epigenomics

DZNE, Germany

 

Lab visit description

Observation of scRNA-Seq experiments. For more information regarding the lab please visit the website: https://www.dzne.de/en/research/precise/

 

Scientific methods offered to the student (any or a combination of the following)

  • scRNA-Seq: SeqWell, Smart-Seq2

 

Duration of lab visit

1 week

Period

Year round - subject to arrangement

Costs covered by lab

Research material

Costs to be covered by participants

Travel costs, accommodation

Required language skills

English

 

Application details

Please include the following information in your application:

  • Name
  • Description of current research topic and motivation for lab visit
  • Name of supervisor
  • Short statement by supervisor why lab visit is beneficial for the applicant
  • CV
  • Copy of highest university degree
  • Copy of passport

 

Applications will be evaluated as soon as they are received. The decision will be based on information provided by the student, the lab's research plan, and the number of other applicants. Administrative prearrangements prior to visit may take 2 months.

 

Application to be sent via email to:

Kristian Händler

kristian.haendler@dzne.de

Simulation Lab Neuroscience, Jülich Supercomputing Centre

Forschungszentrum Jülich, Germany

 

Lab visit description

The SimLab Neuroscience at Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich is an interdisciplinary team of scientists and engineers with complementary backgrounds and skills, dedicated to supporting neuroscientists in using high-performance computing (HPC) and data resources for their research. Expertise in both neuroscience and HPC is based on in-house research and development, as well as collaborative joint projects with the Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, and other national and international partners. It is an active partner in multiple HBP work packages. JSC is also one of the Fenix hosting sites.

The SimLab offers students an insight into the world of HPC and how HPC can be efficiently used for neuroscience research, from modelling and simulation to data analysis and neuroimaging. Visiting students should have some programming skills, e.g. in C, C++ or Python, to be able to use their visit for a (first) project with HPC and/or data resources. Short-term visits allow a student to join SimLab experts in their everyday work; longer-term stays offer the opportunity to actively contribute to one of the SimLab projects or to work on an own project.

JSC offers a number of (free) training courses throughout the year. A Lab Visit could be combined with the attendance of one or multiple courses, e.g. an introduction to the supercomputing resources at the institute or an introduction to GPU programming.
 

The SimLab Neuroscience experts also supervise Bachelor and Master projects. Students who are searching for a hosting lab for their thesis, should mention this in their application.
 

One of the SimLab Neuroscience teams takes care of coordination, management and dissemination of projects, e.g. for the HBP Work Package 6 (EBRAINS Computing Services) and the Interactive Computing E-Infrastructure (ICEI) project, which is creating the Fenix Infrastructure for the HBP and other science communities. Interested Students should mention their interest to work with this team in their application.
 

Scientific methods offered to the student

A detailed list of the research topics and projects of the SimLab Neuroscience can be found on our website.

  • High Performance Computing
  • Simulators and simulation engineering, e.g.
  • Development of the simulators Arbor, NEST, The Virtual Brain
  • Structural plasticity
  • Parameter exploration
  • Modular science: complex interactive workflows on supercomputers
  • Data analysis and visualisation, e.g.
  • Visualization-guided interactive graph analysis
  • Interactive steering and visualisation
  • Visual connectivity generation
  • Neuroimaging pipelines, e.g.
  • Deep Learning for brain extraction from MRI scans
  • Deep Learning for image segmentation of 3D-PLI images
     
Duration of lab visit 3 days to a couple of weeks
Period At any time (provided that the potential supervisor is available)
Costs covered by lab
  • Computing time
  • Workstation (for longer-term stays)
Costs to be covered by participants
  • Travel costs
  • Accommodation (SimLab Neuroscience offers support to find an affordable place, in particular for longer-term stays, e.g. at the Forschungszentrum Jülich guesthouse)
  • Notebook (in particular for shorter-term stays)
Required language skills English


 

Application details

Please include the following information in your application:

  • Name
  • Current supervisor, if any*
  • Short description of programming skills
  • Short description of current project
  • Motivation for the lab visit
  • List of publications, if any
  • Preferred timeframe for the lab visit, e.g. “up to 4 weeks in July-September 2021”

*Students who currently do not have a supervisor can nevertheless apply
 

Please include the following documents in your application:

  • Letter of motivation
  • CV
  • Short statement by supervisor why a lab visit is beneficial for the applicant


Applications are reviewed as they arrive.

The SimLab team leaders will review every application together to identify one or multiple SimLab teams that the student could visit, and check if these teams have enough manpower to supervise a visiting student in the envisaged timeframe. If a lab visit can be offered, the SimLab will then get in contact with the student to sort out the details of the stay.


Application to be sent via email to:

Prof. Dr. Abigail Morrison
slns@fz-juelich.de