- Comp-neuro - lists.cnsorg.org

Survey of user experiences in modeling

by Anton Arkhipov

Dear Colleagues, Our NIH BRAIN Initiative-sponsored project (1U24NS124001) is conducting an annual survey of the needs and experiences of users in neuroscience modeling. Would you be so kind to help us by filling out this brief survey? https://www.surveymonkey.com/r/2023NeuralModelingSoftware It will take only 5 minutes, and the results will help guide future development of software and documentation for the community. Whether you use our tools or not, an expert or novice in modeling, we’d love to hear from you! Thank you so much. If you have any questions, please feel free to reach out by email. Best regards, Anton. Anton Arkhipov Investigator E: antona(a)alleninstitute.org<mailto:antona@alleninstitute.org> [Text Description automatically generated] alleninstitute.org<https://alleninstitute.org> brain-map.org

May 30, 2023

Postdoc positions in ML/Neuro at Tübingen University

by Jakob Macke

Dear colleagues, We have several openings for Postdoctoral Researchers to work at the intersection of Machine Learning and Computational Neuroscience funded by the ERC Consolidator Grant “DeepCoMechTome: Using deep learning to understand computations in neural circuits with Connectome-constrained Mechanistic Models“. The goal of DeepCoMechTome is to develop simulation-based machine learning tools that will make it possible to build neural network models that are both biologically realistic and computationally powerful. Some relevant prior work can be found in https://www.biorxiv.org/content/10.1101/2023.03.11.532232v1. We are looking for candidates with a strong quantitative background and PhD in a relevant discipline, ideally in computational neuroscience, machine learning or numerical simulation, a genuine interest in collaborative work at the interface of machine learning and neuroscience, and strong programming skills (ideally Python and relevant deep learning frameworks). Our research group (https://www.mackelab.org <https://www.mackelab.org/>) develops methods in machine learning and artificial intelligence to accelerate scientific discovery, with a particular focus on neuroscience. We aim to provide an interdisciplinary, collaborative and supportive work environment which emphasizes diversity and inclusion. We are embedded in Tübingen’s internationally renowned research community in artificial intelligence and computational neuroscience, including the Cyber Valley Initiative, the Tübingen AI Center, the ELLIS initiative, the Excellence Cluster Machine Learning, the Bernstein Center for Computational Neuroscience, the Hertie Institute for AI in Brain Health and dedicated MSc Programs in Machine Learning and Computational Neuroscience. We are situated in the AI Research Building, in close proximity to the Max Planck Institutes for Intelligent Systems and Biological Cybernetics, and participate in the two International Max Planck Research Schools (IMPRS) `Intelligent Systems’ and`Mechanisms of Mental Function and Dysfunction’. The University of Tübingen is committed to equal opportunity, diversity and inclusion. In case of equal qualification and experience, physically challenged applicants are given preference. The University of Tübingen aims at increasing the share of women in science and highly encourages female scientists to apply. We also explicitly encourage scientists from outside Germany to apply. Please submit your application materials to mls-jobs(a)inf.uni-tuebingen.de <mailto:mls-jobs@inf.uni-tuebingen.de>, including a CV with publication list, a statement of research interests (max. two pages), contact details of two referees, and a link to a code repository (or work samples). Application deadline is June 20, 2023. Candidates are encouraged to send their application material early, as we will start reviewing applications before the deadline. Initial fixed-term contracts will be for 3 years at level E13 TV-L with possible extensions, starting date is flexible. Part-time positions are possible. Hiring is carried out by the Central Administration. For further details and instructions, see www.mackelab.org/jobs <http://www.mackelab.org/jobs>. Best, Jakob Macke Prof. Dr. Jakob Macke Machine Learning in Science; Cluster of Excellence "Machine Learning”, University of Tübingen Adjunct Senior Research Scientist, Department of Empirical Inference; Max Planck Institute for Intelligent Systems Tübingen Director, Bernstein Center for Computational Neuroscience www.mackelab.org <http://www.mackelab.org/>

May 26, 2023

Fully funded PhD Opportunity: Brain Dynamics and Motor Skill Learning in Surgery - deadline 8 June 2023

by aomurtag

An exciting PhD studentship position available in the Engineering department at Nottingham Trent University, United Kingdom, for highly competitive candidates with excellent qualifications. Application deadline: 8th of June 2023. Project title: Brain Dynamics and Motor Skill Learning in Surgery The project involves the use of EEG and fNIRS recordings from task performing human subjects and Matlab programming and signal analysis in order to discover patterns related to cognitive load and motor skill. For more information: NTU link: https://lnkd.in/gfbiYQRM Find-a-phd link: https://lnkd.in/gQgPrUiE Application instructions: https://lnkd.in/grUFevV5

May 25, 2023

Call for Abstracts for the Bernstein Conference 2023 in Berlin - Contributed talks and posters

by Bernstein Communication

Call for Abstracts for the Bernstein Conference 2023 in Berlin - Contributed talks and posters +++ The Bernstein Network Computational Neuroscience invites proposals for Contributed Talks of the Bernstein Conference 2023 in Berlin. +++ ____ Each year the Bernstein Network invites the international computational neuroscience community to the annual Bernstein Conference for intensive scientific exchange. It has established itself as one of the most renown conferences worldwide in this field, attracting students, postdocs and PIs from around the world to meet and discuss new scientific discoveries. www.bernstein-conference.de ____ IMPORTANT DATES * Bernstein Conference: September 26 - 29, 2023 * Deadline for submission of abstracts to be considered for Contributed Talks: June 21, 2023 * Deadline for poster abstract submission: July 19, 2023 ____ ABSTRACTS We invite the computational neuroscience community to submit their abstracts: Submitted abstracts can either be considered as contributed talks or posters. All accepted abstracts will be published online and will be citable via Digital Object Identifiers (DOI). Further information can be found here: https://bernstein-network.de/bernstein-conference/abstract-submission/<https://bit.ly/BC_submission> ____ INVITED SPEAKERS Keynote Marlene Cohen (University of Chicago, USA) Invited Talks Tiago Branco (Sainsburry Wellcome Center, UK) Stefano Fusi (Columbia University, USA) Ann Kennedy (Northwestern University, USA) Julija Krupic (University of Cambridge, UK) Wiktor Mlynarski (Institute of Science and Technology, Austria / LMU Munich, Germany) Adrien Peyrache (McGill University, Canada) Kanaka Rajan (Icahn School of Medicine at Mount Sinai, USA) Christopher Summerfield (University of Oxford and Deepmind, UK) Julia Veit (Albert-Ludwigs-Univesität Freiburg, Germany) ____ CONFERENCE COMMITTEE Robert Gütig (Conference Chair) Tatjana Tchumatchenko (Program Chair) Srdjan Ostojic (Program Vice Chair) Anna Levina (Workshop Chair) Maria Eckstein (Workshop Vice Chair) & Athena Akrami, Ann Hermundstad, Mehrdad Jazayeri, Christian Leibold, Ashok Litwin-Kumar, Ida Momennejad, Nicole Rust, Andrew Saxe, Daniela Vallentin, Friedemann Zenke. ____ For any further questions, please contact: bernstein.conference(a)fz-juelich.de -- Dr. Dorthe Kaufhold Scientific Management and Coordination Bernstein Network Computational Neuroscience | Bernstein Coordination Site Branch Office of the Forschungszentrum Jülich at the University of Freiburg Hansastr. 9a | 79104 Freiburg, Germany phone: +49 761 203-9589 mail: bernstein.communication(a)fz-juelich.de<mailto:bernstein.communication@fz-juelich.de> web: www.bernstein-network.de<http://www.bernstein-network.de> Twitter: BernsteinNeuro Mastodon: BernsteinNetwork(a)mastodon.world<mailto:BernsteinNetwork@mastodon.world> LinkedIn: Bernstein Network Computational Neuroscience, Germany ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

May 25, 2023

PhD position - Model-predictive control of brain plasticity for optimal non-invasive brain stimulation

by Caroline Lea-Carnall

We are looking for a PhD student to come and work with us at the University of Manchester. Please get in touch via the link below if you are interested! About the Project Neuroplasticity is the mechanism that underpins the brain’s ability to learn or recover from traumatic events, but also its deterioration underlies several Neurodegenerative diseases and mental illnesses. It is an umbrella term that encompasses multiple processes occurring at different spatial and temporal scales (1, 2). The most commonly discussed type of plasticity is long-term potentiation (LTP) which is defined as an increase in efficacy between synapses of two neurons. Experiments designed to measure LTP are often done in cell slices or cultures using patch-clamp techniques. However, we often want to promote (and measure) plasticity in humans in-vivo but it is not clear how changes in synaptic efficacy manifest in macroscopic non-invasive imaging measurements such as magnetic resonance imaging (MRI), magnetic resonance spectroscopy (MRS), or electroencephalography (EEG) that are available for use in humans. This project aims to link our detailed cellular-level knowledge of plasticity processes with systems-level observations in humans and is focused on answering the following 2 questions: 1. How can we modulate plasticity non-invasively in the brain? 2. How can we measure plasticity in vivo? To answer these questions you will combine mathematical/computational modelling of biophysically realistic large-scale neural networks that exhibit plasticity with cutting-edge neuroimaging techniques to test the model predictions. The model will be adapted so that its output can be compared to the three major imaging techniques described above and you will determine how changes in connectivity between and within brain regions in the model predict changes in our imaging metrics. There will be a particular focus on developing an EEG marker of plasticity as this currently does not exist. Finally, you will test the model predictions in an imaging study combining brain stimulation, EEG, MRI and MRS in a proof-of-concept experiment in humans. This will provide us with a deeper understanding of how to modulate and measure plasticity that can be deployed in the future for medical applications of brain stimulation such as in Parkinson’s disease, depression and pain control. Link to project: https://www.findaphd.com/phds/project/epsrc-dtp-model-predictive-control-of…

May 25, 2023

PhD and postdoc positions to investigate the biophysical basis of neural computation with machine learning

by pedro goncalves

Dear all, Our lab was recently founded at the Neuro-Electronics Flanders (NERF), Belgium. We are currently exploring a range of exciting topics at the intersection between computational neuroscience and probabilistic machine learning. In this context, we are looking for a PhD and a postdoc interested in using computational tools to investigate how the complex biophysics of single neurons gives rise to the dynamics of neural populations. These projects will make use of our previously developed machine learning methods, and depending on the selected candidates' interests, can involve further method development. More details about the positions and the lab can be found at http://jobs.vib.be/j/57438 http://jobs.vib.be/j/57439 Best wishes, Pedro Gonçalves --------------- Pedro Gonçalves Principal Investigator at NERF, a joint research initiative by imec, VIB, and KU Leuven https://goncalveslab.sites.vib.be/en

May 24, 2023

Information theory workshop at CNS*2023 -- call for contributed talks

by Joseph Lizier

Dear all, We are pleased to announce that the Workshop on Methods of Information Theory in Computational Neuroscience<https://bit.ly/cns2023itw> will be held once again at the 32nd Annual Computational Neuroscience Meeting (CNS*2023<http://www.cnsorg.org/cns-2023> conference), in Leipzig, Germany. The workshop will be held during sessions over the final two days of the main conference, July 18 and 19, 2023. Our confirmed speakers so far include the following: * Jürgen Jost, Max Planck Institute for Mathematics in the Sciences, Leipzig * Sarah Marzen, Claremont Colleges, USA * Demian Battaglia, University of Strasbourg * Marilyn Gatica, University of Nottingham * Pedro Mediano, Imperial College London * Nadine Spychala, Univeristy of Sussex * Andreas C. Schneider, Max Planck Institute for Dynamics and Self-Organization, Göttingen * ... more TBA! We would like to <https://abzinger.github.io/202307-CNS2023-ITW.html#call> call for further contributions<https://bit.ly/cns2023itwcall> of talks. If you are interested in contributing a talk, please send a title and abstract to Abdullah Makkeh (abdullah.alimakkeh(a)uni-goettingen.de<mailto:abdullah.alimakkeh@uni-goettingen.de>). Earlier submissions and those from female/minority speakers will be prioritised. Please pay attention to the registration for CNS*2023 (deadlines and fees) as workshop registration at least is required for attendance, and see our website https://bit.ly/cns2023itw for more details. We hope you will join us there! Organising Committee: Abdullah Makkeh (co-chair) Michael Wibral (co-chair) Joseph Lizier Pedro Mediano

May 23, 2023

CfP: The 16th International Conference on Brain Informatics (BI'23)

by Feng Liu

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ CALL FOR PAPERS The 16th International Conference on Brain Informatics (BI'23) August 1 - 3, 2023 Hoboken & New York – USA The key theme: Brain Science meets Artificial Intelligence Conference homepage: wi-consortium.org/conferences/bi2023/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ *** IMPORTANT DATES *** - 24 May 2023: Full Paper Submission Deadline - 01 Jun 2023: Abstract Submission Deadline *** Confirmed Keynote Speakers *** - Professor Emery N. Brown Member of the National Academy of Sciences Member of the National Academy of Engineering Member of the National Academy of Medicine MIT, Massachusetts General Hospital, USA - Professor Bin He Fellow of International Academy of Medical and Biological Engineering (IAMBE) Fellow of American Institute of Medical and Biological Engineering (AIMBE) Fellow of Biomedical Engineering Society (BMES), and IEEE Member of the National Academy of Inventors Carnegie Mellon University, USA - Professor John Ngai Director of NIH BRAIN Initiative NIH BRAIN Initiative, USA - Professor Helen Mayberg Member of the National Academy of Sciences Member of the National Academy of Medicine Member of the National Academy of Inventors Member of the American Academy of Arts and Sciences Mount Sinai Medical Center, USA - Professor Vinod Goel Author of monographs: “Sketches of thought” and “Reason and Less: Pursuing Food, Sex, and Politics” York University, Canada - Professor Amy Kuceyeski Director of Computational Connectomics (CoCo) at Weill Cornell Medicine Cornell University, USA - Dr. Grace Hwang Director, NINDS, NIH *** Local information *** *The location of the BI2023 in the beautiful campus of Stevens Institute of Technology in Hoboken, New Jersey, located on the west bank of Hudson River overlooking Manhattan. Stevens is close to a group of finest universities such as Princeton University (1.5 hours drive), Columbia University (25 min drive), New York University (20 min drive) and Yale University (1h 40 min drive). *Convenient transportation: (1) Nearby there are three major airports: Newark, JFK, and LaGuardia with direct flights to all major cities in the world. (2) 15 minutes to Time Square by bus. *An economic accommodation option: $100 dorm room option is available in the newly completed University Complex Center Building with a view of Manhattan (limited spaces) ***About the conference*** The International Conference on Brain Informatics (BI) series has established itself as the world's premier research conference on Brain Informatics, which is an emerging interdisciplinary and multidisciplinary research field that combines the efforts of Cognitive Science, Neuroscience, Machine Learning, Data Science, Artificial Intelligence (AI), and Information and Communication Technology (ICT) to explore the main problems that lie in the interplay between human brain studies and informatics research. The 16th International Conference on Brain Informatics (BI'23) provides a premier international forum to bring together researchers and practitioners from diverse fields for presentation of original research results, as well as exchange and dissemination of innovative and practical development experiences on Brain Informatics research, brain-inspired technologies and brain/mental health applications. *** Topics and Areas *** The key theme of the conference is "Brain Science meets Artificial Intelligence". The BI'23 solicits high-quality original research and application papers (full paper and abstract presentation submissions). Relevant topics include but are not limited to: Track 1: Cognitive and Computational Foundations of Brain Science Track 2: Human Information Processing Systems Track 3: Brain Big Data Analytics, Curation and Management Track 4: Informatics Paradigms for Brain and Mental Health Research Track 5: Brain-Machine Intelligence and Brain-Inspired Computing ***Journal Opportunities*** High quality BI conference papers may be nominated to submit an extended version for a fast track review and publication at the Brain Informatics Journal (https://braininformatics.springeropen.com/) an international, peer-reviewed, interdisciplinary Open Access journal published by Springer Nature. Real-time Journal's Impact Factor: 8.5. *** Paper Submission and Publications *** Submission link: http://wi-consortium.org/conferences/bi2023/paper%20submissions%20and%20pub… 9-12 pages are encouraged for the regular papers including figures and references in Springer LNCS Proceedings format ( https://www.springer.com/us/computer-science/lncs/conference-proceedings-gu…) Overlength pages will be charged 200$ per page. All papers will be peer-reviewed and accepted based on originality, significance of contribution, technical merit, and presentation quality. All papers accepted (and all workshop & special sessions' full length papers) will be published by Springer as a volume of the Springer-Nature LNAI Brain Informatics Book Series ( https://link.springer.com/conference/brain) Abstract Presentation Submission: Submission link: http://wi-consortium.org/conferences/bi2023/paper%20submissions%20and%20pub… Research abstracts are encouraged and will be accepted for presentations in an oral presentation format and/or poster presentation format. Each abstract submission should include the title of the paper and an abstract body within 1500 words. Note: The abstract will not be included in the conference proceedings to be published by Springer. Special Issues & Books: Workshop organizers can be invited to contribute a book publication in the Springer-Nature Brain Informatics & Health Book Series ( https://www.springer.com/series/15148) or a special issue at the Brain Informatics Journal. *** Workshop & Special Sessions *** Proposal Submissions: BI'23 will be hosting a series of workshops and special sessions featuring topics relevant to the brain informatics community on the latest research and industry applications. Papers & Presentations: A workshop/special session typically takes a half day (or full day) and includes a mix of regular and invited presentations including regular papers, abstracts, invited papers as well as invited presentations. The paper and abstract submissions to workshops/special sessions will follow the same format as the BI conference papers and abstracts. Proposal Guidelines: Each proposal should include: 1) workshop/special session title; 2) length of the workshop (half/full day); 3) names, main contact, and a short bio of the workshop organizers; 4) brief description of the workshop scope and timeline; 5) prior history of the workshop (if any); 6) potential program committee members and invited speakers; 7) any other relevant information

May 22, 2023

Open position: Postdoctoral position in Human Visual Psychophysics with fMRI/MRI, Tuebingen, Germany

by Pavlovic, Maria

Postdoctoral position in Human Visual Psychophysics with fMRI/MRI, (m/f/d) (TVöD-Bund E13, 100%) The Department of Sensory and Sensorimotor Systems (PI Prof. Li Zhaoping) at the Max Planck Institute for Biological Cybernetics and at the University of Tübingen is currently looking for highly skilled and motivated individuals to work on projects aimed towards understanding visual attentional and perceptual processes using fMRI/MRI. The framework and motivation of the projects can be found at: <https://www.lizhaoping.org/zhaoping/AGZL_HumanVisual.html> https://www.lizhaoping.org/zhaoping/AGZL_HumanVisual.html. The projects can involve, for example, visual search tasks, stereo vision tasks, visual illusions, and will be discussed during the application process. fMRI/MRI technology can be used in combination with other methods such as eye tracking, TMS and/or EEG methodologies, and other related methods as necessary. The postdoc will be working closely with the principal investigator and other members of Zhaoping's team when needed. Responsibilities: * Conduct and participate in research projects such as lab and equipment set up, data collection, data analysis, writing reports and papers, and presenting at scientific conferences. * Participate in routine laboratory operations, such as planning and preparations for experiments, lab maintenance and lab procedures. * Coordinate with the PI and other team members for strategies and project planning. * Coordinate with the PI and other team members for project planning, and in supervision of student projects or teaching assistance for university courses in our field. Requirements: * Ph.D. in neuroscience, psychology, computer science, physics or a related natural science or engineering field. * Publications in peer-reviewed journals. * Highly skilled in techniques of human visual psychophysics such as eye tracking, MATLAB programming for experiments, experimental data taking, data analysis, and paper writing. * Highly skilled in fMRI experiments and data analysis. * Experience in project management is highly desired. * Strong command of English; knowledge of German is a plus. Who we are: We use a multidisciplinary approach to investigate sensory and sensory-motor transforms in the brain (www.lizhaoping.org <http://www.lizhaoping.org> ). Our approaches consist of both theoretical and experimental techniques including human psychophysics, fMRI imaging, EEG/ERP, and computational modelling. One part of our group is located in the University, in the Centre for Integrative Neurosciences (CIN), and the other part is in the Max Planck Institute (MPI) for Biological Cybernetics as the Department for Sensory and Sensorimotor Systems. You will have the opportunity to learn other skills in our multidisciplinary group and benefit from interactions with our colleagues in the university, at MPI, as well as internationally. This job opening is for the CIN or the MPI working group. The position (salary level TVöD-Bund E13, 100%) is for a duration of two years. Extension or a permanent contract after two years is possible depending on situations. We seek to raise the number of women in research and teaching and therefore urge qualified women to apply. Disabled persons will be preferred in case of equal qualification. Your application: The position is available immediately and will be open until filled. Preference will be given to applications received by July 31th, 2023. We look forward to receiving your application that includes (1) a cover letter, including a statement on roughly when you would like to start this position, (2) a motivation statement, (3) a CV, (4) names and contact details of three people for references, (5) if you have them, transcripts from your past and current education listing the courses taken and their grades, (6) if you have them, please also include copies of your degree certificates, (7) you may include a pdf file of your best publication(s), or other documents and information that you think could strengthen your application. Please use pdf files for these documents (and you may combine them into a single pdf file) and send to jobs.li(a)tuebingen.mpg.de <mailto:jobs.li@tuebingen.mpg.de> , where also informal inquiries can be addressed. Please note that applications without complete information in (1)-(4) will not be considered, unless the cover letter includes an explanation and/or information about when the needed materials will be supplied. For further opportunities in our group, please visit <https://www.lizhaoping.org/jobs.html> https://www.lizhaoping.org/jobs.html _________________________________ Maria Pavlovic Assistant to Prof. Zhaoping Li Office Hours: 07.00-13.00 Max Planck Institute for Biological Cybernetics Max-Planck-Ring 8 D-72076 Tuebingen phone +49 7071 601 609 fax +49 7071 601 619 <mailto:maria.pavlovic@tuebingen.mpg.de> maria.pavlovic(a)tuebingen.mpg.de <http://www.lizhaoping.org/> www.lizhaoping.org

May 22, 2023

Modellers Workshop for the Brain Dynamics Toolbox

by Stewart Heitmann

Enrolments for the Modeller's Workshop are now open Master the art of programming differential equations in Matlab with the Brain Dynamics Toolbox. This online course is for researchers, students and instructors who wish to use the toolbox to build their own dynamical models. Every step of the process is demonstrated in a short video lecture with a practical focus on programming techniques. Topics include programming Ordinary Differential Equations, Partial Differential Equations, Delay Differential Equations, Stochastic Differential Equations, Auxiliary Plot Functions and command-line tools. Example code is provided in all cases. Study time is 8 hours. Course Website https://bdtoolbox.teachable.com/p/modellers-workshop Toolbox Website https://bdtoolbox.org Important Information The course is limited to 25 students. Enrolments close Sun 11th Jun 2023. Textbook Heitmann & Breakspear (2022) Handbook for the Brain Dynamics Toolbox: Version 2022. ISBN 978-0-6450669-2-0. Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.

May 21, 2023