August 2024 - Comp-neuro - lists.cnsorg.org

Python Package: Kuramoto model

by Fabrizio Damicelli

Dear Computational Neuroscience Community, I would like to point you to a potentially useful Python Package,especially in the realm dynamical models and synchronization phenomena. The Kuramoto model is used to study a wide range of systems (for a review on its usage in the Neuroscience, see Breakspear et al. 2010, Generative models of cortical oscillations: neurobiological implications of the Kuramoto model) "kuramoto": Python implementation of the Kuramoto model. [https://opengraph.githubassets.com/676ee08440b553afd4448323a4a8244abc846110…]<https://github.com/fabridamicelli/kuramoto> GitHub - fabridamicelli/kuramoto: Python implementation of the Kuramoto model<https://github.com/fabridamicelli/kuramoto> Python implementation of the Kuramoto model. Contribute to fabridamicelli/kuramoto development by creating an account on GitHub. github.com  * Code: (https://github.com/fabridamicelli/kuramoto) * Easy install with `pip install kuramoto` * Example notebooks: https://github.com/fabridamicelli/kuramoto/tree/master/examples * A super concise intro to the model and its behaviour and further references can be found here: https://github.com/fabridamicelli/kuramoto#kuramoto-model-101 As of today, a few people already trust it and the package registers >27K total downloads, ~900/month (pypi.org) Check it out and any feedback/suggestions/bug reports are more than welcome (simply open an issue: https://github.com/fabridamicelli/kuramoto/issues) All the best, Fabrizio Damicelli

Aug. 8, 2024

Call for Papers: The First Workshop on NeuroAI @ NeurIPS 2024, Vancouver, CA

by Forough Habibollahi

*Call** for Papers: The First Workshop on NeuroAI @ NeurIPS 2024: Fusing Neuroscience and AI for Intelligent Solutions* We are excited to announce that we are organizing* the First Workshop on NeuroAI @ NeurIPS 2024*, which will showcase research at the intersection of neuroscience and artificial intelligence. This workshop aims to bring together leading researchers to present their latest findings in NeuroAI. *Topics of Interest:* - Explainable and interpretable AI in neuroscience - Self-supervised systems in NeuroAI - Neuro-inspired architectures, and computations - Neuronally-plausible learning regimes - Neuro-inspired reasoning and decision-making - Cognitive functions in AI The topics above are NOT exhaustive, and we encourage the submission of research related to how principles and insights from neuroscience can lead to better artificial intelligence and vice versa. Our aim is to foster groundbreaking interdisciplinary research that advances both fields. *Submission Details:* We invite researchers in the field of NeuroAI to submit their papers to this workshop. Submissions should adhere to a page limit of *5 pages *(excluding references and supplementary materials) and must use the NeurIPS 2024 LaTeX template <https://media.neurips.cc/Conferences/NeurIPS2024/Styles.zip>. Authors are encouraged to submit their NeurIPS main conference submissions concurrently to this workshop (excluding any completed and already published work). *Important Dates:* · Submission Deadline: September 7, 2024 · Submission Portal: NeuroAI Workshop Submission Portal <https://openreview.net/group?id=NeurIPS.cc/2024/Workshop/NeuroAI> *The top 4 highly scored submissions will be chosen for spotlight talks.* *Event Details:* · Date: During NeurIPS 2024, 14 or 15 December 2024 (to be confirmed) · Location: In-person in Vancouver, Canada *Enquiries:* For further information, please contact: neuroai.neurips2024(a)gmail.com For more information about the details of the workshop schedule, lineup of speakers, etc. and to stay updated, please check the workshop website: NeuroAI Workshop Website <https://neuroai-workshop.github.io/> We look forward to your submissions and to seeing you at *NeurIPS 2024*! *On behalf of the NeuroAI workshop organizing committee,* *Moein Khajehnejad, **Forough Habibollahi, **Adeel Razi, **Jason Eshraghian, Noor Sajid, Anthony Zador, Yoshua Bengio*

Aug. 8, 2024

Application deadline extended: Advanced Neural Data Analysis and Neuroinformatics School (ANDA-NI)

by Michael Denker

There are still spots available for the Advanced Neural Data Analysis and Neuroinformatics school (ANDA-NI)! Interested in learning more on how to analyze complex cellular and network-level neuroelectrophysiological data in Python using hands-on exercise on the data you care about? Then hurry to apply for the remaining spots! Some of the topics covered: correlation analysis, variability, dimensionality reduction, spectral analysis, causality, data sharing and data representations New extended application deadline: *August 21, 2024* For more information and application procedures, please visit our school application page at https://andani.info

Aug. 6, 2024

new book: Electric Brain Signals

by Gaute Einevoll

We are very pleased to announce our new book: Electric Brain Signals Cambridge University Press, 2024 AUTHORS Geir Halnes, Norwegian University of Life Sciences Torbjørn V. Ness, Norwegian University of Life Sciences Solveig Næss, University of Oslo Espen Hagen, University of Oslo Klas Pettersen, Norwegian Artificial Intelligence Research Consortium Gaute Einevoll, Norwegian University of Life Sciences BOOK DESCRIPTION It is common to study the electric activity of neurons by measuring the electric potential in the extracellular space of the brain. However, interpreting such measurements requires knowledge of the biophysics underlying the electric signals. Written by leading experts in the field, this volume presents the biophysical foundations of the signals as well as results from long-term research into biophysics-based forward-modeling of extracellular brain signals. This includes applications using the open-source simulation tool LFPy, developed and provided by the authors. Starting with the physical theory of electricity in the brain, this book explains how this theory is used to simulate neuronal activity and the resulting extracellular potentials. Example applications of the theory to model representations of real neural systems are included throughout, making this an invaluable resource for students and scientists who wish to understand the brain through analysis of electric brain signals, using biophysics-based modeling. REVIEWS ‘Electric Brain Signals, by the Norwegian group founded by Gaute Einevoll, is the definitive how-to guide for detailed, biophysical modeling of brains, building up from the minuscule ionic currents traversing the cellular membrane, to the observed macro-variables across spatial scales, from the extracellular action potential and local field potential to EEG and MEG signals recorded inside or outside the skull. The book beautifully encapsulates, with easy-to-read prose and associated code, the sophistication of quantitative, mechanistic neuroscience of the twenty-first century necessary to understand the brain and the mind at the time scale of sensory input, motor action, and thought, in both health and disease.’ Christof Koch - Allen Institute for Brain Science, USA; and author of Biophysics of Computation ‘If you love physics, are fascinated with the brain, and wish that neural circuits could be understood from first principles, this book is for you! Gaute Einevoll and his team put together a masterpiece educational resource. Depending on the background and stage of training, the reader can consume it front to back, or use it as a reference book. The first part covers, in detail, the biophysical theory governing generation of the transmembrane and extracellular electrical potential. The second part is a comprehensive guide to simulations of these signals with the focus on data-driven modeling, from the microscopic level of single neurons and neural networks to macroscopic signals observable with noninvasive electro- and magneto-encephalography. This didactic organization, depth of coverage, and impeccable expertise of the authors make this book a top candidate as a textbook for computational neuroscience courses. Supplementary simulation software, freely available on GitHub, is a fantastic addition for research and teaching.’ Anna Devor - Boston University, USA ‘The brain is an electrochemical organ. The laws of electricity are simple. Yet how currents spread in a heterogeneous, non-isotropic milieu, such as the brain, is super complex. This long needed outstanding book provides all the necessary ingredients to comprehend this complexity. Done with the utmost care, this volume is a must-read for both novices and experts in electrophysiology and I bet it will become the foundation of elective graduate courses for many years to come. The text is the systems neuroscience equivalent of the single-neuron Hodgkin–Huxley model.’ György Buzsáki - NYU Neuroscience Institute, USA; and author of Rhythms of the Brain and The Brain from Inside Out ‘This book is a fantastic resource for the computational neuroscience community and beyond. The introductory ‘guide’ is outstanding in its clarity and description for readers with a range of backgrounds. The presentation is rigorous and detailed with many mathematical equations, and yet readable and understandable, with many figures. The authors are to be commended for their clearly defined terminologies and presentation of complex concepts. A gem of a read for anyone wanting to develop an in-depth understanding of electrical brain recordings and models of them.’ Frances K. Skinner - Krembil Brain Institute, University Health Network and University of Toronto, Toronto, Ontario, Canada https://www.cambridge.org/core/books/electric-brain-signals/900A8A211004B98… [https://assets.cambridge.org/97813165/10841/large_cover/9781316510841i.jpg]<https://www.cambridge.org/core/books/electric-brain-signals/900A8A211004B98…> Electric Brain Signals<https://www.cambridge.org/core/books/electric-brain-signals/900A8A211004B98…> Cambridge Core - Biological Physics and Soft Matter Physics - Electric Brain Signals www.cambridge.org ******************************* Professor Gaute T. Einevoll Department of Physics, Norwegian University of Life Sciences, 1432 Aas, Norway; Department of Physics, University of Oslo, 0316 Oslo, Norway theoretical neuroscience podcast: theoreticalneuroscience.no<https://theoreticalneuroscience.no> popular science podcast: vettogvitenskap.no<https://vettogvitenskap.no> popular science podcast (English only): vettogvitenskap.no/senseandscience<https://vettogvitenskap.no/senseandscience> Co-author of "Electric Brain Signals": www.cambridge.org/electricbrainsignals<http://www.cambridge.org/electricbrainsignals> Co-author of "Principles of computational modeling in neuroscience" (2nd ed): www.cambridge.org/sterratt2<http://www.cambridge.org/sterratt2/> mobile: +47-95124536 email: Gaute.Einevoll(a)nmbu.no<mailto:Gaute.Einevoll@nmbu.no>, Gaute.Einevoll(a)gmail.com Twitter: @gauteeinevoll Blue Sky: @gauteeinevoll.bsky.social Zoom: https://nmbu.zoom.us/my/gauteeinevoll “If you sleep in a democracy, you may wake up with a dictator.”

Aug. 6, 2024

PhD position in Göttingen: Optogenetics in the Retina and Computational Neuroscience

by Gollisch, Tim

A PhD position is available in the lab of Tim Gollisch at the University Medical Center Göttingen, Germany. The PhD project will investigate how optogenetics can be used for vision restoration therapy to treat blindness. The work will involve multielectrode arrays to record spiking activity from isolated retinas of mice that express light-sensitive ion channels in different cell types of the retina. Furthermore, computational tools will be used for model-driven data analysis and assessment of neural coding under optogenetic stimulation. Prior experience with electrophysiology or computational analyses/computer programming will be considered advantageous for the application. The project is part of the newly founded Else Kröner Fresenius Center for Optogenetic Therapies (https://ekfz.uni-goettingen.de/) and will contribute to bringing optogenetic vision restoration towards clinical trials and patient treatment. Furthermore, the research group is embedded in the strong and lively neuroscience research community of Göttingen, including the university, several Max Planck Institutes, the German Primate Center, and the European Neuroscience Institute. We are also part of the Bernstein Center for Computational Neuroscience Göttingen. To get a better idea about the research group, see https://www.retina.uni-goettingen.de/. For more information or in case of questions, please send an email to Prof. Tim Gollisch (tim.gollisch(a)med.uni-goettingen.de<mailto:tim.gollisch@med.uni-goettingen.de>). For the official application, please visit https://ekfz.uni-goettingen.de/job.html#PhD and follow the instructions there, and mention in your application that you would like to join Team 2 (Vision), as there are multiple positions available in different teams. The University Medical Center Göttingen is an equal opportunities employer, and women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment.

Aug. 6, 2024

PhD position at Charité Berlin on modeling deep brain stimulation with network science

by Meier, Jil Mona

Dear all, for the collaborative research center “ReTune” starting from now on limited for 3 years we are looking for a Ph.D. Candidate (d/f/m) in part-time (25,35 h/week) The position is in the context of the project “Towards clinical application of virtual deep brain stimulation”, funded by the German Research Foundation within the collaborative research center “ReTune” (https://sfb-retune.de/en/home/) The project, led by me (Dr. Jil Meier), aims to model deep brain stimulation (DBS) from a network science perspective, exploring a novel approach for predicting neuromodulation effects based on network control theory. If succesful, the modeling-based DBS predictions will be combined with computational neuroscience approaches to test the benefits of the modeling-suggested DBS programming on Parkinson’s disease patients in a clinical pilot trial. The position is part of the collaborative research center “ReTune” and thus offers a high degree of interaction with other groups of this consortium. In addition, the CRC has an active early-career network, offering various activities, such as Fall Schools, Hackathons and method-training seminars. In more local aspects, the position will be within the Brain Simulation Section (https://www.brainsimulation.org/bsw) at the Berlin Institute of Health at the Charité-Universitätsmedizin Berlin, which is an interdisciplinary group of researchers with various backgrounds headed by Prof. Petra Ritter. More details below or at https://jobs.bihealth.org/PhD-Candidate-dfm-de-j586.html Application deadline is 02.09.2024. If you have any technical questions about the job posting, please contact me (jil-mona.meier(a)bih-charite.de<mailto:jil-mona.meier@bih-charite.de>). Kind regards, Dr. Jil Meier ------------------------------ What you can expect: * application of methods from network science and network control theory to understand the pathology of Parkinson's disease and DBS therapy effects * analysis of various imaging and electrophysiological data sets from healthy controls and Parkinson's disease patients * presentation of results and preparation of scientific publications * development of a modeling-based approach for improved programming for deep brain stimulation devices * collaboration with project partners within the ReTune consortium What you bring along: * Completed scientific university degree (Master, Diploma or comparable) in a relevant field (for example engineering, mathematics, physics, computer science, neuroscience or related fields) * strong interest in neuroscience and neuromodulation, especially deep brain stimulation * ambition to pursue an academic career * high level of motivation and the ability to work both inde-pendently and within a team * ideally experience in mathematical modeling, graph the-ory/network science and (network) control theory and previous experience in working with imaging or electrophysiological data is considered a plus * Very good skills in written and spoken English and foundational knowledge of a programming language (ideal: previous experience with either Matlab or Python) What we offer you: * A varied job in a forward-looking research institute * Remuneration up to TVöD VKA-K EG E13, taking into account personal requirements * Additional benefits customary in the public sector (including annual special payment, company pension scheme (VBL), capital-forming benefits) * Flexible working hours and the option of working remote * 30 vacation days per year (with a five-day week) * Various support offers to balance work and family life (childcare, cooperation with voiio) * Very good training and further education opportunities * Mobile citizens' office on site * Corporate benefits (travel, leisure, shopping, etc.), Charité Gympass, bicycle leasing or abonnement (JobRad, mylo) * Very easily accessible and attractive workplace at CCM, (Robert-Koch-Platz 4, 10117 Berlin) We live diversity! We welcome applications from people with diverse backgrounds, regardless of gender, nationality, ethnic and social origin, religion and ideology, disability, age, sexual orientation and identity. Applications from women are expressly encouraged. Severely disabled and equivalent applicants will be given special consideration if they have the same qualifications and suitability. We believe that diverse teams representing a wide range of experiences, perspectives and backgrounds enrich our research and work. Please submit your application via the BIH career portal (https://jobs.bihealth.org/) with a letter of motivation, CV and relevant work and degree certificates by 02.09.2024, quoting the reference number BIH-65.24. Note: If you have a foreign degree, please submit proof of recognition of your degree in Germany with your application. The proof can be obtained via the anabin database. Please note that it may be necessary to obtain a certificate assessment from the ZAB. You can find more information at: https://www.kmk.org/zab/central-office-for-foreign-education.html Proof of measles immunity / measles vaccination is a prerequisite for employment for those born after 1970. You can find more information on the BIH at https://www.bihealth.org/en/

Aug. 6, 2024

Postdoc position in Human Intracranial Single-Unit Electrophysiology and Brain Stimulation at the University of Magdeburg

by Ciliberti, Davide /DZNE

Dear all, We have an open position for a Postdoctoral researcher in the area of human intracranial electrophysiology, using single-unit recordings and electrical brain stimulation, to study the dynamics of human memory formation and consolidation. More details about the position are available at: https://iknd.med.ovgu.de/Jobs/Postdoctoral+researcher+position.html More information about the research in my group is available at: https://iknd.med.ovgu.de/AG+Dr_+Ciliberti.html To apply, please send your CV, motivational letter and the contacts of three referees to Dr. Davide Ciliberti (davide.ciliberti(a)med.ovgu.de<mailto:davide.ciliberti@med.ovgu.de> ). Informal inquiries or preliminary applications (without referees) are welcome. Best regards, Davide Ciliberti Davide Ciliberti, PhD Junior Research Group Leader ……………………………………………………………………… Institute of Cognitive Neurology and Dementia Research (IKND) Otto-von-Guericke-Universität Medical Faculty Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) c/o Universitätsklinikum Magdeburg Leipziger Str. 44 Building 64, Room 506 39120 Magdeburg Germany

Aug. 5, 2024

PhD position in Human Intracranial Single-Unit Electrophysiology and Brain Stimulation at the University of Magdeburg

by Ciliberti, Davide /DZNE

Dear all, a PhD student position in the area of Human Intracranial Single-Unit Cognitive Electrophysiology and Brain Stimulation is available at the University of Magdeburg (Germany) in my group. Please find the details below. Institution Institute of Cognitive Neurology and Dementia Research (IKND) of the Medical Faculty at the Otto-von-Guericke University Magdeburg. Location University Hospital Magdeburg, Magdeburg, Germany. Supervisors Dr. Davide Ciliberti and Prof. Dr. med. Emrah Düzel. Duration 4 years. Overview The Cognitive Electrophysiology and Neurotechnology (CEN) group at IKND led by Dr. Davide Ciliberti (https://iknd.med.ovgu.de/AG+Dr_+Ciliberti.html) invites applications from highly motivated candidates to fill in a position for a PhD student salary. The successful candidate will have the opportunity to conduct multi-disciplinary research in human neuroscience and neurotechnology. In particular, the successful candidate will investigate the dynamics of formation of human memory using intracranial single-unit electrophysiological recordings, high resolution 7-Tesla imaging and invasive electrical brain stimulation in neurosurgical epilepsy patients. Project Description The aim of the main project is to characterize the behavioral and electrophysiological effects of deep-brain stimulation (DBS) in the human entorhinal cortex during the formation of spatial and non-spatial episodic memory. The research will involve: * designing cognitive tasks for investigating the neurophysiological dynamics of mnemonic discrimination; * recording local field potentials and single-unit activity from intracranial electrodes in neurosurgical epilepsy patients during the execution of cognitive tasks; * applying DBS to the entorhinal cortex during the execution of cognitive tasks; * applying existing analysis techniques and developing new ones for understanding how DBS alters mnemonic discrimination; * applying image segmentation techniques on 7-T MRI data to localize intracranial electrodes with high-resolution. Key Responsibilities * Interacting with patients and record intracranial electrophysiological data. * Conduct high-quality research in cognitive electrophysiology and neuroengineering, by validating or disproving current theories about human episodic memory formation and maintenance. * Collaborate with a multidisciplinary team of researchers, including PhD students, postdocs, medical technicians and doctors. * Present research findings at national and international meetings, and publish results in high-visibility scientific journals. Requirements * A Master degree in Cognitive Neuroscience, Physics, Cognitive Psychology, Biomedical Engineering, Computational Neuroscience or a closely related field. * Basic to intermediate knowledge of a programming languages (e.g. Python, Matlab, C/C++). * Expertise in at least two of the following areas (unless coming from a non-neuroscientific field): * brain stimulation, * human neuroanatomy and neuroimaging, * clinical neurophysiology, * analysis of single-unit activity, * analysis of local field potentials, * theories of episodic memory, * design of cognitive tasks for humans, * brain-computer interfaces. * Analytical, problem-solving, and communication skills. * Inquisitive mindset and critical thinking. * Ability to work independently and as part of a team. * Good command of written and spoken English. * Intermediate to advanced knowledge of German language is highly appreciated (but not required). Benefits * Opportunity to work in a leading research institution with access to state-of-the-art facilities. * Collaborative environment with experts in neuroimaging, electrophysiology, clinical neurophysiology, data analysis, AI, aging research. * Competitive salary (65% TVL E13). * Comprehensive training and career development support (through the OvGU graduate academy). How to apply Please send your CV, a motivational letter and the contacts of two referees to Dr. Davide Ciliberti (davide.ciliberti(a)med.ovgu.de<mailto:davide.ciliberti@med.ovgu.de>). Transcripts of Bachelor and/or Master degree(s) indicating relevant coursework taken will be appreciated (but are not required). Informal inquiries are welcome. Davide Ciliberti, PhD Junior Research Group Leader ……………………………………………………………………… Institute of Cognitive Neurology and Dementia Research (IKND) Otto-von-Guericke-Universität Medical Faculty Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) c/o Universitätsklinikum Magdeburg Leipziger Str. 44 Building 64, Room 506 39120 Magdeburg Germany

Aug. 5, 2024

Modellers Workshop for the Brain Dynamics Toolbox

by Stewart Heitmann

Enrolments are now open for the Modellers Workshop for the Brain Dynamics Toolbox. This is an online course for researchers who wish to build custom dynamical models in matlab using the Brain Dynamics Toolbox. The course focuses on practical programming techniques for the major classes of differential equations (ordinary, partial, delay, stochastic) in computational neuroscience. Example code is provided in all cases. Study time is 8 hours. Upon completion, students will be able to turn differential equations into working simulations. Course Website https://bdtoolbox.teachable.com/p/modellers-workshop Toolbox Website https://bdtoolbox.org Important Dates Enrolments close 31st Aug 2024. 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.

Aug. 5, 2024

Post-doctoral position - Mass Eye & Ear / Harvard Med School

by Maison, Stephane F.,AUD, PhD

A NIH-funded postdoctoral position is immediately available in Dr. Stéphane Maison’s laboratory in the Department of Otolaryngology – Head & Neck Surgery at the Massachusetts Eye & Ear – Harvard Medical School. Our research interests focus on identifying biomarkers of a large range of etiologies and their associated disorders including difficulties hearing and communicating in noisy environments, reduced sound level tolerance and tinnitus using a test battery based on behavioral, electrophysiologic, and psychophysical measures. Salary and benefits are consistent with NIH guidelines and institution policies based on applicant’s experience. Highly motivated candidates who recently graduated with a PhD in biomedical engineering, computational biology, hearing science, neuroscience, or other related fields are welcome to apply. The applicant should have strong programming skills (e.g., Matlab, Python), independent and productive. Experience with human testing is preferred but not required. The fellow will receive an appointment at Massachusetts Eye and Ear and Harvard Medical School. Interested applicants should apply using the following link: https://partners.taleo.net/careersection/mee/jobdetail.ftl?job=3299643&tz=G… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Aug. 4, 2024