June 2023 - Comp-neuro - lists.cnsorg.org

DPG - Bad Honnef Physics School on "Physics of Viruses" this September

by Viola Priesemann

Dear all, we are organizing a Bad Honnef Physics School on "Physics of Viruses" from September 10th till 15th 2023. - This school will cover all aspects of the physics of viruses, from their molecular architecture and assembly through to virus transmission, spread and evolution. We have put together a diverse program with world-renowned speakers, which also includes tutorials and time for discussions and networking. The physics center in Bad Honnef is a fantastic venue for such events and participation fees are very affordable (200 EUR, 100 EUR for DPG-members, covering board and lodging for one week at the Physikzentrum at Bad Honnef, which is close to Bonn and beautifully located at the Rhine). We very much look forward to interacting with interested master students, PhD-students, postdocs and even more senior researchers! You may also bring a poster on your own work and/or contribute a short presentation. More information and the schedule for the school can be found here : https://www.dpg-physik.de/veranstaltungen/2023/physics_of_viruses?set_langu…. Space is limited, so please secure your spot at the school as soon as possible. We very much look forward to welcoming you in Bad Honnef! Best regards, Ulrich Schwarz and Sarah Köster PS: PIs, please forward this email to your group members! https://www.dpg-physik.de/veranstaltungen/2023/physics_of_viruses?set_langu… ---------------------- Tel. +49 (2224) 9232-0 Fax +49 (2224) 9232-50 E-Mail: dpg(a)dpg-physik.de www.dpg-physik.de www.linkedin.com/company/dpgphysik www.facebook.com/DPGPhysik www.instagram.com/DPGPhysik www.youtube.com/DPGPhysikTV Deutsche Physikalische Gesellschaft e. V. Geschäftsstelle, Hauptstraße 5, 53604 Bad Honnef Hauptgeschäftsführer: Dr. Bernhard Nunner Eingetragen beim Vereinsregister des Amtsgerichts Siegburg unter Registernummer VR 90474

June 28, 2023

NEURON, NetPyne, and TREES at OCNS 2023 in Leipzig

by McDougal, Robert

Join us at CNS 2023 in Leipzig on July 15th for the tutorial T01: Building mechanistic multiscale models with NEURON, NetPyNE, and TREES. NEURON is a simulator for neurons and networks of neurons with strong support for morphologically detailed models. TREES is a toolbox for working with morphologies, and NetPyNE is an abstraction layer on top of NEURON to facilitate the specification of large network models. We will talk about both basic and new features. This tutorial will be highly interactive, focusing on cloud-based examples for the NEURON and NetPyNE portions. Registration for the tutorials at CNS 2023 is required and can be done at: https://ocns.memberclicks.net/cns-2023-registration Speakers include: Bill Lytton, Robert McDougal, Thomas Künzel, Hermann Cuntz, Adam Newton, and Salvador Dura-Bernal. Full details are available at: https://cns2023.sched.com/event/150df23f7af1dcca6e55694eba15bf83 Hope to see you there!

June 27, 2023

Apply now for the Computational Neuroscience Imbizo 2024 - form closes 11th July

by Christopher Currin

Dear all, The DEADLINE for the next IMBIZO is approaching very quickly. Don’t let this opportunity slip by if you are hoping to join the most diverse neuroscience summer school at the most beautiful beach in the world! If you know anyone who would benefit from an extraordinary computational neuroscience summer school, please distribute this information as widely as you can: IBRO-SIMONS COMPUTATIONAL NEUROSCIENCE IMBIZO #Imbizo2024 7 January - 28 January 2024, Noordhoek Beach, Cape Town, South Africa http://imbizo.africa/ Application deadline: 11th July 2023 The #Imbizo2024 is a southern hemisphere summer school aiming to promote computational neuroscience in Africa. It will bring together international and local students under the tutelage of the world's leading experts in the field. Like its international sister courses, this four-week summer school aims to teach central ideas, methods, and practices of modern computational neuroscience through a combination of lectures and hands-on project work. Mornings will be devoted to lectures on topics across the breadth of computational neuroscience, including experimental underpinnings and machine learning analogues. The rest of the day will be spent working on research projects under the close supervision of expert tutors and faculty. Individual research projects will focus on the modelling of neurons, neural systems, behaviour, the analysis of state-of-the-art neural data, and the development of theories to explain experimental observations. It also includes a week focused on neuroscience-inspired machine learning! Who should apply? This course is aimed at Masters and early-PhD level students though Honours or advanced undergraduates may also apply. Postdoctoral students who can motivate why the course would benefit them are also encouraged to apply, Students should have sufficient quantitative skills, (e.g. a background in mathematics, physics, computer science, statistics, engineering or related field). Some knowledge of neural biology will be useful but not essential. Experimental neuroscience students are encouraged to apply, but should ensure that they have a reasonable level of quantitative proficiency (i.e. at least second-year level mathematics or statistics and have done at least one course in computer programming). Essential details * Fee (which covers tuition, lodging, and meals): 1350 EUR Thanks to our generous sponsors, significant financial assistance is available to reduce and waiver fees for students, particularly for African applicants. We also hope to provide some travel bursaries for international students. If you are in need of financial assistance to attend the Imbizo, please state so clearly in the relevant section of your application. The Imbizo is planned to be hosted in person, with everyone following our COVID policy <https://imbizo.africa/covid-policy/>. If it is unsafe to hold the summer school, we will follow up with further information at the appropriate time. * Application deadline: 11th July 2023 * References submitted: 14th July 2023 * Notification of results: August 2023 Information and application https://imbizo.africa/ Questions? isicn.imbizo(a)gmail.com What is an Imbizo? \ɪmˈbiːzɒ\ | Xhosa - Zulu A gathering of the people to share knowledge. Incl. past FACULTY and TAs such as... Adrienne Fairhall - Washington University Alex Pouget - University of Geneva Anne-Marie Oswald - University of Pittsburgh Annik Carson - AI Redefined Arif Hamid - University of Minnesota Medical School Aza Allsop - Yale University Bard Ermentrout - University of Pittsburgh Bianca Jones Marlin - Columbia University Blake Richards - McGill University Brent Doiron - University of Chicago Cengiz Pehlevan - Harvard University Christopher Currin - Institute of Science and Technology Austria & IndabaX South Africa Daniela Vallentin - Max Planck Institute for Biological Intelligence David Sussillo - Google Demba Ba - Harvard University Dongyan Lin - MILA Evan Schaffer - Columbia University Franck Kalume - University of Washington Grace Lindsay - New York University Guillaume Lajoie - University of Montreal & MILA Henning Sprekeler - Technical University of Berlin Ilenna Jones - Harvard University Joseph Raimondo - University of Cape Town Mackenzie Mathis - EPFL Lausanne Marjorie Xie - Columbia University Mohamed Abdelhack - Krembil Centre for Neuroinformatics Nina Kudryashova- University of Edinburgh Peter Latham - University College London Rachael Dangarembizi - University of Cape Town Roy Eyono - MILA Spiros Chavlis - IMBB-FORTH SueYeon Chung - New York University Thomas Tagoe - University of Ghana Tim Vogels - Institute of Science and Technology Austria Timothy Lillicrap - DeepMind Xaq Pitkow - Baylor College of Medicine ORGANISERS Demba Ba (Harvard University) Christopher Currin (Institute of Science and Technology Austria & IndabaX South Africa <https://indabax.co.za>) Peter Latham (Gatsby Unit for Computational Neuroscience) Joseph Raimondo (University of Cape Town) Emma Vaughan (Imbizo Logistics) Tim Vogels (Institute of Science and Technology Austria) Sponsors The Imbizo is made possible by the generous support from the Simons Foundation <https://www.simonsfoundation.org/>, the International Brain Research Organisation (IBRO) <https://ibro.org/> as well as the Wellcome Trust, Google Deep Mind and others. Organizational Affiliates University of Cape Town, University College London, Institute of Science and Technology Austria, TReND in Africa <http://trendinafrica.org/>, Neuroscience Institute <http://www.neuroscience.uct.ac.za/>, Gatsby Foundation <http://www.gatsby.org.uk/>, IBRO African Center for Advanced Training in Neurosciences at UCT

June 27, 2023

Open research training: Open Seeds mentoring & training program is open for application until July 2023

by Mayya Sundukova

Dear all, The next cohort of Open Seeds OLS-8 is open for application! Open Seeds is a Mentoring & Training Programme run by OLS, designed for people interested in applying open principles in their work and becoming Open Science ambassadors in their communities. The program is free but requires registration in OpenReview and an application with a project where you would like to apply open skills. More information: https://openlifesci.org/ The deadline to apply is on July 7th, with a decision made in August and the cohort starting in mid-September 2023. On the 28th of June OLS will run an open webinar “Application Clinic (Q&A)” where interested participants can ask the OLS team any questions about their applications to the program. If you have not thought about a project and application, this can be an excellent opportunity to learn more about the program and get inspired https://www.eventbrite.co.uk/e/application-clinic-call-qa-tickets-660976427… . Help us share about the Open Seeds OLS-8 call in your network. More about Open Seeds Purpose: Training for individuals and teams interested in furthering their Open Science skills in any area of research and community projects. Process: Online 16-week with online cohort calls and mentor-based individual support to help participants in integrating open science practices in their work and in the long term become Open Science ambassadors in their community. Open leaders from Open Seeds OLS programme are - taught essential knowledge required to create, lead, and sustain an Open Science project. - connected with members across different communities, backgrounds, and identities by creating space in this program for them to share their experiences and expertise. - empowered to become effective Open Science ambassadors in their communities. *Examples of projects you can bring:* Please see our previous cohorts for a full list of projects that have been developed in OLS: OLS1 <https://openlifesci.org/ols-1/projects-participants/>, OLS-2 <https://openlifesci.org/ols-2/projects-participants/>, OLS-3 <https://openlifesci.org/ols-3/projects-participants/>, OLS-4 <https://openlifesci.org/ols-4/projects-participants/>, OLS-5 <https://openlifesci.org/ols-5/projects-participants/>, OLS-6 <https://openlifesci.org/ols-6/projects-participants/> and OLS-7 <https://openlifesci.org/ols-7/projects-participants/> - Researchers and data scientists: applying open, reproducible and FAIR principles to their current research, data management plan, collaborative workflow design, tooling and roadmapping, the publication of research outcome, a side project they are working on, an app they are building for social good, a prototype they want to further enhance etc. - Business team members: collaborative projects with the researcher, public engagement, dissemination of research output, community engagement, survey and feedback collection, infrastructure design, resource hosting services etc. - Support staff members: data management, reproducible workflow, FAIRification of research components (training, data, web source etc.), support documents for their colleagues, participatory & citizen science - Community/project managers: community-building skills, community development project, collaborative research, training and education opportunity etc. To learn more about the program and process of application, you can check the recording of the application launch call from the previous cohorts on the OLS YouTube channel: https://youtu.be/shM2mVyLjxU For additional details, feel free to reach out to the Open Life Science team at: team(a)openlifesci.org. We are also on social media: - Twitter: https://twitter.com/openlifesci - Linkedin: https://www.linkedin.com/company/openlifesci/ - Youtube channel with open educational resources: https://www.youtube.com/@OpenLifeSci <https://www.youtube.com/@OpenLifeSc>. We look forward to welcoming you in the next cohort. Best wishes, OLS Team

June 26, 2023

Call for community review: 2 new neuroscience SBPs

by INCF

Two calls for community review: 1. Digital SWC Reconstructions Describing Neuron Morphology (SWC) 2. SPARC Data Structure Feedback from the community is an important part of our review process; it helps us ensure that the standard has community support and is useful and practical to the community. By commenting, you contribute to improving the standard for current and future users! 1. Digital SWC Reconstructions Describing Neuron Morphology (SWC) SWC files (file extension of .swc) are text-based (ASCII text) files that describe three-dimensional neuronal or glial morphology. These digital reconstructions represent morphology as a vectorized tree structure, made of a series of connected nodes. An SWC file contains a series of text-based rows where each neuron node is described by a single row of only seven space-separated values. The format is simple and intuitive; a parser of or writer to the format could be implemented by anyone with knowledge of any programming language. With an open archive and freely available structure editor, the SWC system facilitates community-wide pooling of data for building biophysically realistic neuronal models and studying the morphological variation between neurons, contributing to a greater neuroscientific cooperation and openness. Review by Aug 15 Learn more: incf.org/commentaries/swc <https://www.incf.org/commentaries/swc> 2. SPARC Data Structure Financially backed by the NIH Common Fund, SPARC is a large-scale project which aims to deepen our knowledge of nerve-organ interactions. With an initial focus on bioelectronic medicine, the SPARC consortium created the SPARC data structure (SDS), a file and metadata organizational scheme inspired by the Brain Imaging Data Structure (BIDS). This data structure has proven capable of handling complex datasets from multiple and heterogeneous species, measurement techniques, and spatial scales. One of the primary purposes of SDS is to increase the integrity of scientific research by promoting FAIR and open science practices, particularly by facilitating the generation of well-annotated, organized, standardized, and shared biomedical datasets. Review by Aug 15 Learn more: incf.org/commentaries/sparc <https://www.incf.org/commentaries/sparc> Thanks for your help! /The INCF Team

June 26, 2023

Computational Neuroscience Postdoc position in New York

by Salvador Dura-Bernal

A Postdoc position is now available in the Dura-Bernal Lab<http://dura-bernal.org/> at the State University of New York (SUNY) Downstate Health Sciences University (Brooklyn, New York), working on a new exciting multidisciplinary project entitled "Restoring motor function after spinal cord injury using multiscale modeling to decode neural latent dynamics from motor cortex EEG." The position is funded by New York State (NYS) Department of Health (DOH) Spinal Cord Injury Research program. The project aims to improve brain-machine interface decoders by combining multiscale modeling of motor cortex circuits, analysis of low-dimensional neural manifolds associated with behavior, and realistic simulation of EEG signals. See our recent Cell Reports publication describing the multiscale motor cortex model and behavior-related neural manifolds: www.cell.com/cell-reports/fulltext/S2211-1247(23)00585-5<http://dura-bernal.org/www.cell.com/cell-reports/fulltext/S2211-1247(23)005…> For more details and how to apply visit: http://dura-bernal.org/postdoc-2023<https://t.co/aGDh79EjyE> (Please share!) ________________________________ The contents of this email message and any attachments are confidential and are intended solely for the addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify sender by reply email or by (718) 270-HELP.

June 25, 2023

Registration for the Bernstein Conference 2023 in Berlin is open now

by Alexander Lammers

***Registration for the Bernstein Conference 2023 in Berlin is open now*** ___ The Bernstein Conference 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 renowned 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<http://www.bernstein-conference.de> ___ Important Dates * Bernstein Conference: September 26 - 29, 2023 * Abstract submission for posters: July 19, 2023, 15:00 CEST * Travel grant applications: July 19, 2023 * Early registration: July 19, 2023 ___ Registration Registration for the Bernstein Conference is open now. Register until July 19, 2023, and profit from reduced conference fees. All information: https://bernstein-network.de/bernstein-conference/registration/ ___ Abstract Submission We invite the computational neuroscience community to submit their abstracts. The abstract submission for posters is open until July 19, 2023, 15:00 CEST. All accepted abstracts will be published online and will be citable via Digital Object Identifiers (DOI). Abstract submission: https://bernstein-network.de/bernstein-conference/abstract-submission/ ___ Travel Grants Students, PhD candidates, and postdocs can apply for travel grants. Travel grant application: https://bernstein-network.de/bernstein-conference/early-career-scientists/t… ___ Invited Speaker Keynote Marlene Cohen (University of Chicago, USA) Invited Talks Tiago Branco (Sainsbury Wellcome Center, UK) Stefano Fusi (Columbia University, USA) Ann Kennedy (Northwestern University, USA) Julija Krupic (University of Cambridge, UK) Wiktor Mlynarski (LMU Munich, Germany / Institute of Science and Technology, Austria) 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. ___ Contact For any further questions, please contact: bernstein.conference(a)fz-juelich.de<mailto:bernstein.conference@fz-juelich.de> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

June 23, 2023

1 PhD position on: New methods for realistic and comfortable experiences in AR

by Agostino Gibaldi

We are inviting applications for one fully funded PhD position (3 years) in the Department of Informatics, Bioengineering, Robotics, and Systems Engineering <https://dibris.unige.it/en>, at the University of Genoa (IT), in collaboration with Magic Leap <https://www.magicleap.com/en-us/>. The research theme focuses on realistic and comfortable experiences in Augmented Reality (more info in the attached call for position). Interested applicants are welcome to reach out for more information about the theme and the position. The official call can be found here: https://unige.it/dottorati-di-ricerca You can apply from June 09 at 03.00 pm (italian time) to July 10 at 12.00 noon (italian time) at this page: https://unige.it/en/students/phd-programmes Best, Agostino Gibaldi, PhD Human Vision Scientist Magic Leap *New methods for realistic and comfortable* *experiences in AR – University of Genoa* *Curriculum: *Industry 4.0 *Hosting Institution: *University of Genoa *Department: *Department of Informatics, Bioengineering, Robotics, and Systems Engineering (DIBRIS) *Tutors:* Silvio P. Sabatini, Andrea Canessa, Gerrit Maus, Agostino Gibaldi *Description:* Optical see-through (OST) augmented reality head-mounted displays (HMD) have emerged as a key asset in several application fields. In OST HMDs the direct view of the world is mostly preserved and there is no perspective conversion in viewpoint and field of view, as with video see-through (VST) systems. This aspect confers a clear advantage over VST solutions, particularly when used to interact with close objects. Although there have been significant improvements to performance and comfort of OST HMDs, limitations associated with human perception still remain to be addressed. In order to provide the user with a realistic, natural and comfortable visual experience, a thorough and accurate knowledge of eye characteristics and HMD geometry must be assumed. These quantities are usually calibrated on a per-device and per-user basis, or modeled from scientific literature. A deviation of the actual values from the expected ones can result in incorrect camera placement, spatial distortions and non-uniformities, thus triggering discomfort in VR/AR. The goal of this research project is to develop methods and techniques to assess and mitigate discomfort and perceptual inconsistencies between real and augmented visual content in OST HMDs. A joint experimental and modeling approach will be followed in order to: 1. investigate methods to evaluate different sources of discomfort/mismatch; 2. develop subjective and objective methods to quantify the originated discomfort; 3. investigate strategies to mitigate the sources of discomfort/mismatch in AR/VR devices. *Requirements:* Applicants are expected to: 1) have a keen interest in Vision Science and in Augmented Reality, 2) have good programming skills in at least one language (Matlab, C/C++, Python, C#), 3) work well in group problem solving situations, 4) have intermediate communication skills (oral and written) in English or better. Experience in Unity 3D is a plus. *References:* [1] Konrad, R., Angelopoulos, A., & Wetzstein, G. (2020). Gaze-contingent ocular parallax rendering for virtual reality. ACM Transactions on Graphics (TOG), 39(2), 1-12 [2] Lambooij, M. T., IJsselsteijn, W. A., & Heynderickx, I. (2007). Visual discomfort in stereoscopic displays: a review. Stereoscopic Displays and Virtual Reality Systems XIV, 6490, 183-195. [3] Gibaldi A., Liu Y., Kaspiris-Rousellis C., Mahadevan M., Vlaskamp B.NS, Maus G.W. Vertical vergence and screen alignment with see-through head-mounted displays. ECVP 2023. *Company name and link (for industrial projects):* Magic Leap Inc. (www.magicleap.com) *Number of positions available: 1* *Main Research Sites* *1.* DIBRIS, via Opera Pia 13, 16145 Genoa, Italy, *2.* Macic Leap Inc., Andreasstrasse 5, 8050 Zürich, Switzerland *Contacts:* Email: silvio.sabatini(a)unige.it, gmaus(a)magicleap.com *Funding Scheme:* This doctorate grant is co-funded by PNRR program DM-117

June 22, 2023

Endowed Professorship "Machine Learning for Clinical Neuroscience"

by Philipp Berens

Dear all, we are currently advertising an Endowed professorship "Machine Learning for Clinical Neuroscience" (https://www.academics.com/jobs/w3-stiftungsprofessur-fuer-maschinelles-lern…) at the University of Tübingen. We are looking for candidates that perform innovative research on the application and development of new machine learning methods in clinical neuroscience, in particular for early detection and prediction of disease progression. This can include work on topics such as explainability, safety and robustness of machine learning methods in clinical settings. It would be great if candidates had worked with multimodal data with clinical relevance (e. g. MRI, fMRI, EEG, electrophysiology, omics data, data from sensors of wearables) as well as cohort data (UKBiobank, NAKO, etc.). Tübingen offers a first-rate environment at the intersection of neuroscience and AI/ML research with the Excellence Cluster for Machine Learning in Science, the Tübingen AI Center, the Max Planck Institutes for Intelligent Systems and Biological Cybernetics, the Hertie Institute for Clinical Brain Research and many other institutions! We are looking forward to your application by July 20th. Best Philipp -- Professor of Data Science, Director Hertie Institute for AI in Brain Health Medical Faculty of the University of Tübingen www.berenslab.org

June 22, 2023

[job post] Open PhD positions on neuromorphic perception and control for soft robots

by Chiara Bartolozzi

We are looking for three PhD fellows interested in developing neuromorphic systems for robots. They will team up to look at the different aspects involved in developing neuromorphic circuits and computation for sensing, perception, and actuation for soft biomimetic robots. We will aim at coupling soft materials, sensory transduction, neuromorphic circuits and computation, and soft actuation, towards the design of robots that can seamlessly and gently interact with their environment. Each PhD will have their own multi-disciplinary research goals and will be co-supervised by leading scientists in the complementary disciplines: Neuromorphic distributed intelligence for soft robots – Computation with spiking neural networks for haptic perception and closed loop control of soft robots – Supervisors: C. Bartolozzi<https://edpr.iit.it/> & B. Mazzolai<https://bsr.iit.it/> Neuromorphic distributed intelligence for soft robots – Design of neuromorphic circuits on flexible substrates for sensing and computation – Supervisors: C. Bartolozzi<https://edpr.iit.it/> & L. Beccai<https://sbrp.iit.it/> Online neuromorphic perception and actuation for robots – Italian Institute of Technology – Supervisors: C. Bartolozzi<https://edpr.iit.it/>, S. Soldado-Magraner<https://bri.ucla.edu/people/saray-soldado-magraner/> & E. Donati<https://services.ini.uzh.ch/people/elisa> Location: Italian Institute of Technology, via San Quirico 19D, Genova, Italy https://iit.it Enrolment: DRIM PhD School @ University of Genova https://drim.i-rim.it/en/ Official call (with guidelines for applications): https://unige.it/en/students/phd-programmes PhD themes description: https://drim.i-rim.it/wp-content/uploads/2023/05/Research-Themes-Hostile-an… - checkout Themes 3,4<https://drim.i-rim.it/wp-content/uploads/2023/05/Research-Themes-Hostile-an…>,5 Deadline for application: June 30th

June 22, 2023