January 2021 - Comp-neuro - lists.cnsorg.org

Registration Deadline is approaching!

by Mary

Dear community, As we are approaching deadline (January 30) for registering for "EEG/ERPs Recording and Analysis: A multifaceted approach to EEG signals" Online Course, here is a reminder for the interested researchers who haven’t been registered yet. The "EEG/ERPs Recording and Analysis: A multifaceted approach to EEG signals" Online Course is going to be held by Dr. Raphaël Fargier, PhD in Cognitive Neuroscience, Université Claude Bernard Lyon 1, France, who is a researcher in cognitive neuroscience with 10 years of experience and his research is focused on semantic cognition and the neurobiology of language. Through the course you will learn about the basics of EEG signal and how to record it. You will learn different approaches to EEG signal processing, that are more or less commonly adopted in cognitive neuroscience, including the study of Event-Related Potentials, Microstates/Topographic patterns, and Brain oscillations. You will learn about EEG signal preprocessing and how to compute ERPs, Microstates and Time-frequency maps in relationship with the constraints linked to experimental manipulations and designs. There will be a heavy focus on critical thinking about the choices of analyses as a function of research questions, challenges depending on experimental designs, and parameters to pay attention to. The variety and appropriateness of statistical methods currently used to validate (or not) hypotheses about cognitive processes will also be discussed. All of that will be evidenced through the presentation and discussion of case studies in electrophysiology of language. At the end of the course, you will know the strengths and weaknesses of these tools, and will be able to decide which measure is best adapted to your own scientific investigations about cognition. Prospective overview of the sessions 1. Basics of EEG signal and EEG recordings * Overview of the theory behind neural signals * Contrasting neuroimaging methods * Presentation of different EEG recording systems and their classical features * Tips on EEG recordings * Principles of experimental designs using EEG in cognitive neuroscience (events, timing etc) 2. EEG pre-processing Goal: Mastering the successive pre-processing steps including principles and challenges of: * Artifact rejection and correction (e.g. ICA; 3D Spline electrode interpolation) * Filtering (e.g. parameters, band widths etc) * Re-referencing (e.g. mastoid, average reference, Laplacian) * single-to-noise and number of trials 3. ERPs * Presentation of classical ERPs as markers of cognitive processes(e.g. N1/P2, P1, N400, etc.) * Computing single-subject and group-average ERPs: Pre-stimulus baseline correction (rationale, parameters, tips) Methods used to extract measures including amplitudes, latencies and topographies of ERPs Methods for statistical evaluation of differences across experimental manipulations * Differences between stimulus-aligned and response-aligned epochs, and associated challenges for signal processing 4. Spatio-temporal segmentation * Origin of microstates * Rationale of Spatio-temporal segmentation (StS) and presentation of successive steps of analyses (e.g. Topography consistency test, Tanova) * Presentation of two ways to compute StS (different toolboxes) and the respective parameters to take care of * Extraction of measures, and statistical evaluations of differences across experimental manipulations via fitting (e.g. global explained variance, duration, presence, etc.) * Single-trials and mixed models 5. Time-frequency analyses * Rationale of oscillatory dynamics in EEG signal (evoked vs. induced activity) * Challenges in pre-processing to obtain time-frequency maps as compared to ERPs * Different methods used for time-frequency decomposition * Challenges of baseline normalization (the case of response-aligned epochs) * The various measures that can be extracted from time-frequency maps and the variety of approaches for statistical validation You can watch the introductory webinar to this course using the linke below: https://sciencebeam.com/raphael-fargier-webinar/ For more information and registration click on the link below: https://sciencebeam.com/eeg-erps-recording-and-analyses/ Don’t miss this opportunity!

Jan. 21, 2021

PhD/Postdoc at the Group for Neural Theory, ENS, Paris

by CAYCO GAJIC Natasha

Dear all, A PhD or postdoctoral position is available in Alex Cayco Gajic's team in the Group Neural Theory, at the ENS, in Paris, France (http://iec-lnc.ens.fr/group-for-neural-theory/ [1]). The project will use recurrent neural networks to understand cerebello-cortical dynamics during motor learning. A component of the project can be to develop analysis tools for broader use in systems neuroscience. The Group for Neural Theory is a highly interactive and dynamic environment situated in central Paris, and embedded within the strong Parisian theoretical neuroscience community. The ideal candidate should have a strong quantitative background, e.g. in computational neuroscience, physics, applied maths, or computer science. Previous experience in neuroscience and/or machine learning is preferred but not required. Starting dates are flexible. Candidates should send a letter of motivation (2 pages max), the contact information of 2 to 3 referees and their CVs to natasha.cayco.gajic at ens.fr [2]. Please feel free to email me with any informal inquiries. Best, Alex https://sites.google.com/view/caycogajic/home Links: ------ [1] http://iec-lnc.ens.fr/group-for-neural-theory/ [2] http://ens.fr/

Jan. 21, 2021

postdoc and PhD position on body schema modeling @CTU Prague

by Matej Hoffmann

* Dear colleagues, there is a postdoc and PhD openingin the humanoid, cognitive, and neurorobotics group (https://cyber.felk.cvut.cz/research/groups-teams/humanoids/) coordinated by Dr. Matej Hoffmann (https://sites.google.com/site/matejhof/) at the Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague. The topics are in the context of a 5-year project entitled “Whole-body awareness for safe and natural interaction: from brains to collaborative robots” for excellence in fundamental research from the Czech Science Foundation (see https://cyber.felk.cvut.cz/news/new-gacr-expro-project <https://cyber.felk.cvut.cz/news/new-gacr-expro-project/>for more information) and include: - Analysis and modeling of infant behavioral data related to reaching, reaching to the self, and mirror self-recognition - Employing humanoid robots with artificial skin to construct embodied computational models of body and peripersonal space representations - Neural network models of multisensory integration and peripersonal space - Social human-robot interaction focusing on touch and interpersonal distance Open positions: Postdoc. The postdoc will independently conduct research and will also be involved in shaping the research of the group and supervising students. The gross salary will be in the range of CZK 50 000-70 000 per month (approx. 2000-2700 EUR) depending on qualification, plus direct bonuses for scientific achievements such as top-tier publications. PhD student. The topic will be co-defined with the student depending on his skills and interests. The standard duration of the PhD study is 4 years. The funding corresponds to a gross salary of CZK 45 000 per month (approx. 1750 EUR), plus direct bonuses for scientific achievements such as top-tier publications. Robots and infrastructure The humanoids group has at its disposal several humanoid robots (iCub, 2 Naos - 1 with whole-body sensitive skin) and collaborative or lightweight manipulators (KUKA LBR iiwa, UR10e with Airskin, Kinova Gen3). Additional infrastructure includes several robot hands (Barrett Hand BH8-282, QB Soft Hand) and grippers, a 3D Motion Capture System, impact measuring devices, etc. The group has also access to the facilities of the Research Center for Informatics such as a high-performance computational cluster. International collaborations There is a large group of international experts who have agreed to act as collaborators/advisors on the project. These include experts in - developmental psychology: Dr. Kevin O’Regan (CNRS, Paris), Prof. Jeffrey J. Lockman (Tulane University, New Orleans) - cognitive psychology and neuroscience: Prof. Matthew Longo (Birkbeck University, London), Prof. Tobias Heed (Bielefeld), Prof. Andrea Serino (University of Lausanne), Dr. Jean-Paul Noel (Center for Neural Science at New York University), Drs. M.Gori and Giulia Cappagli (Italian Institute of Technology, Dr. S. Signorini (IRCSS Fondazione Mondino Pavia) - physical human-robot interaction: Prof. Sami Haddadin (TU Munich), Dr. Arash Ajoudani (Italian Institute of Technology), Dr. Michael Zillich (Blue Danube Robotics – manufacturer of Airskin) - social human-robot interaction: Dr. Alessandra Sciutti (Italian Institute of Technology), Dr. Hagen Lehmann (University of Macerata) Prague There is currently a very lively international ecosystem in the areas of robotics and AI - at the Department and in Prague in general. See, for example, http://rci.cvut.cz/or https://prg.ai/en/. How to apply. The application should include: -Motivation letter (max. 1 page) - CV (including 2 reference persons) -1 Letter of recommendation (can be from 1 of the reference persons above) Please send the applications or inquiries to matej.hoffmann(a)fel.cvut.czwith (“PhD application” or “postdoc application” in the subject). The positions are open until filled. Best regards, Matej Hoffmann * -- Matej Hoffmann, PhD Assistant Professor Department of Cybernetics Faculty of Electrical Engineering Czech Technical University in Prague https://sites.google.com/site/matejhof/home +420 224 357 387

Jan. 20, 2021

survey for a standardized format for model exchange

by Nichol W. Killian

Hello Colleagues, We recently received funding, as part of the NSF Convergence Accelerator Program (https://www.nsf.gov/od/oia/convergence-accelerator/) for a multi-investigator project that aims to develop a standardized format for exchanging and executing computational models developed by researchers in cognitive science, neuroscience, and machine learning. As part of the project, we have constructed a brief survey to gauge the computational model usages from various domains/communities, and the value that such an exchange format would have. We would greatly appreciate it if you would take a few moments to provide us with information regarding the modeling environments you use frequently, and the benefits and/or challenges you would see for developing such an exchange format. https://docs.google.com/forms/d/e/1FAIpQLSfOZSyoWL4J_MfHTIq5Jx0dnJSVHNFH7UP… [https://lh5.googleusercontent.com/fPzuVxv5E-g2xfDpxYbODDYX68AiT6zcn5yTW4XB-…]<https://docs.google.com/forms/d/e/1FAIpQLSfOZSyoWL4J_MfHTIq5Jx0dnJSVHNFH7UP…> Computational modeling survey<https://docs.google.com/forms/d/e/1FAIpQLSfOZSyoWL4J_MfHTIq5Jx0dnJSVHNFH7UP…> docs.google.com Data from this survey will only be used for informational query and will not be shared with outside sources/marketing companies. The survey is anonymous, unless you chose to add an email address for follow-up correspondence. Please also feel free to convey the link to this survey to others (in your lab or other colleagues) who you believe could provide useful feedback. Thank you for contributing to our project and to furthering the science. - Jonathan Cohen, Princeton Neuroscience Institute Nichol Killian Research Project Coordinator Princeton Neuroscience Institute Princeton University

Jan. 20, 2021

Virtual Event Announcement: Symposium on Explanation in Neuroscience and Artificial Intelligence (SENAI)

by Jessica Thompson

Symposium on Explanation in Neuroscience and Artificial Intelligence (SENAI) Join us on *Wednesday February 10th, 2021* for a virtual symposium on philosophical and scientific approaches to Explanation in Neuroscience and Artificial IntelligenceSpeakers: - Ida Mommenejad, Microsoft Research - John Krakauer, Johns Hopkins University - Andrew Saxe, Oxford University - Lotem Elber-Dorozko, Hebrew University - Rosa Cao, Stanford University - Cameron Buckner, University of Houston Themes: - Reductionism & emergence - Representation & computation - Explanation & understanding Details online: https://sites.google.com/mila.quebec/senai/homeRegister for free and view the event: https://www.crowdcast.io/e/senai2021/register

Jan. 19, 2021

ikerbasque postdoctoral fellows: track towards permanent position

by Serafim Rodrigues

Dear all, Ikerbasque, the Basque Foundation for Science, has launched a new international call to reinforce research and scientific careers in the Basque Country. In particular it announces the following: - 20 positions for experienced postdoctoral researchers Ikerbasque Research Fellows (see link <https://calls.ikerbasque.net/?_mrMailingList=132&_mrSubscriber=65&utm_campa…> ) - 5-year contracts, during the last year the researcher can be assessed to obtain a permanent contract - PhD degree between Jan2010 - Dec2018 As leader of the Mathematical Computational and Experimental Neuroscience (MCEN) research line I would like to support candidates for these positions Potential candidates: Please send before Feb 9th 2021 the following information: - updated CV and two reference letters to: srodrigues(a)bcamath.org With kind regards Serafim -- Serafim Rodrigues Group Leader *BCAM - *Basque Center for Applied Mathematics Alameda de Mazarredo, 14 E-48009 Bilbao, Basque Country - Spain Tel. +34 946 567 842 srodrigues(a)bcamath.org | www.bcamath.org/srodrigues *(**matematika mugaz bestalde)*

Jan. 18, 2021

Postdoc in Neural Data Science @ Tübingen for 3 years

by Philipp Berens

Dear all, we, the “Data Science for Vision Research” group at the Institute for Ophthalmic Research at the University of Tübingen (www.berenslab.org) is offering a position for a postdoctoral researcher (100%, TV-L E13) in Neural data science for initially three years to start as soon as possible. We are looking for a motivated and enthusiastic person with a PhD in computational neuroscience, machine learning or related fields with a strong interest in applying modern machine learning approaches for deciphering the neural circuits of the retina. The ideal candidate should be interested in working on combining detailed simulations of neurons with machine learning techniques, e.g. for parameter inference, methods for processing two-photon calcium or voltage imaging data, the analysis of spatial transcriptomics data of neural tissues or related topics. Further topics of interest in the lab include machine learning techniques for analyzing single-cell transcriptomics data as well as machine learning for medical image analysis. Applications should include a CV and a motivation letter – let us know why you are excited about your previous research and how you would want to work with us. Members of underrepresented groups are particularly encouraged to apply – currently, we are a diverse team from eight different countries with a reasonable gender ratio, and we are excited to receive your application! Please send your application materials as a single pdf to philipp.berens(a)uni-tuebingen.de. The application deadline is February 15th and applications will be evaluated until the position is filled. https://jobrxiv.org/job/data-science-for-vision-research-lab-university-of-… -- Professor of Data Science for Vision Research Institute for Ophthalmic Research, University of Tübingen Cluster of Excellence "Machine Learning - New Perspectives for Science" www.berenslab.org

Jan. 18, 2021

Tutorial on Modeling Tools: BMTK and SONATA

by Anton Arkhipov

Dear colleagues, Please join us for an online tutorial at the Allen Institute. Tools for modeling: The Brain Modeling Toolkit and SONATA data format January 28, 2021 | 10:00-11:00am PT Please register here: https://alleninstitute.org/what-we-do/brain-science/events-training/open-fo… The Brain Modeling Toolkit is a Python-based open software package for building, simulating, and analyzing large-scale neural network models. It supports the building and simulation of models at various scales. Dai et al., PLOS Comp. Bio., 2020a<https://doi.org/10.1371/journal.pcbi.1008386> The Brain Modeling Toolkit is linked to SONATA, a standardized data format for storing networks and simulations. Dai et al., PLOS Comp. Bio., 2020b<https://doi.org/10.1371/journal.pcbi.1007696> These are the software tools we used to build, simulate, and share our multi-scale models of mouse V1, which are freely available to the community. Billeh et al., Neuron, 2020<https://doi.org/10.1016/j.neuron.2020.01.040> https://portal.brain-map.org/explore/models We are looking forward to seeing you there. Anton Arkhipov Associate Investigator T: 206.548.8414 [cidimage001.png(a)01D5B043.A5662590] www.alleninstitute.org<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.alleni…>

Jan. 18, 2021

PhD position in decision-making at University of Balearic Islands

by Catalina Vich Llompart

A 3 year PhD student position starting on March-April 2021 is offered to work with Dr. Catalina Vich at Universitat de les Illes Balears (UIB), together with Dr. Jonathan Rubin at University of Pittsburgh (UPitt), and Dr. Tim Verstynen and Dr. Eric Yttri at Carnegie Mellon University (CMU). The PhD student will be involved in an international project between USA and Spain to investigate circuit-level mechanisms of adaptive decision-making. They will engage in research on learning algorithms in spiking networks with an emphasis on cortico-basal ganglia-thalamic networks and the role of dopamine, as well as on the relation between spiking dynamics and abstract decision-making frameworks. Required skills from the PhD student: We are looking for highly motivated and self-driven candidate with strong interest and experience in computational neuroscience and significant computational expertise. To be accepted in the PhD program, a MSc degree is required preferably in mathematical biology, computational biology or related disciplines. Students who do not hold a MSc degree but hold an undergraduate degree of 300ECTS are also encouraged to apply. A high level of written and spoken English and good programming skills (python and C) are essential. The accepted candidate will be mentored, supervised and trained by C.Vich, J. Rubin and T.Verstynen, and they will have to occasionally visit the USA team (when pandemic safety restrictions are lifted). Environment The Universitat de les Illes Balears (https://www.uib.eu <https://www.uib.eu/>) is located in Mallorca, the highest island of the Balearic Islands, at the foot of the Tramuntana mountains, an area declared a World Heritage Site by the UNESCO, as well as being just a few kilometres from Mallorca’s finest beaches. It is also ranked among the top 5 Spanish universities in innovation and technological development and in research quality. The university is well connected with the main city, Palma, and other villages. It has good transport links to the whole of the archipelago. In fact, it has a bus and underground service with good timetables and frequencies. The accepted student will be a member of the group of Dynamical Systems (SSDD, http://www.ssdd.uib.es <http://www.ssdd.uib.es/>) and the institute of Applied Computing and Community Code (IAC3, http://iac3.uib.es <http://iac3.uib.es/>), with ample opportunities to interact with other young researchers in the fields of physics and mathematics in a highly interactive, dynamic, and multi-cultural environment. Salary Salary will be arranged in accordance to the University salaries for this purpose, which is around 16.000€/year (before TAX). To apply All applicants have to send their Curriculum Vitae, two letters of recommendation and an application letter expressing their interest to Dr. Catalina Vich at catalina.vich(a)uib.es <mailto:catalina.vich@uib.es> with subject “Phd position”. An interview may take place during the selection process. Documents can be written in either English, Catalan or Spanish. Applications will be accepted until the 15th of February. An objective rubric system will be used to score applications for the position, to avoid implicit bias. An online interview might be request. All qualified applicants will receive consideration for employment without regard to race, religion, sexual orientation, nationality, disability, etc. Demographic and cultural diversity will be considered in the selection of the trainee. __________________________ Dr. Catalina Vich Llompart Universitat de les Iles Balears

Jan. 14, 2021

Postdoc position: Modeling age-related cognitive decline in rhesus monkeys (Boston, MA)

by Christina M. Weaver

*Computational Neuroscience postdoc position: Modeling mechanisms of age-related cognitive decline in rhesus monkeys* A postdoctoral research fellowship in computational neuroscience is available immediately with the interdisciplinary research team led jointly by Dr. Jennifer Luebke (Dept of Anatomy & Neurobiology, Boston University School of Medicine, Boston MA), Dr. Christina Weaver (Dept of Mathematics, Franklin & Marshall College, Lancaster, PA), and Dr. Patrick Hof (Dept of Neuroscience, Icahn School of Medicine at Mount Sinai, New York NY). The central goal of the NIH-funded project is to characterize changes in the prefrontal cortex and visual cortex during normal aging in the rhesus monkey, to gain insight into mechanisms that contribute to age-related cognitive decline. The successful candidate will build computational models of cortical networks that incorporate age-related changes to individual neurons, and explore mechanisms of network dysfunction. The models will be constrained by our morphology, physiology, and behavior studies in rhesus monkeys, including new multiplexing data in collaboration with GE Healthcare. Our joint publications related to this project include Ibañez et al. *Front. Comput. Neurosci.* (2020), PMID 32009920; Rumbell et al., *J. Comput. Neuro*. (2016), PMID 27106692; and Amatrudo et al., *J. Neurosci.* (2012), PMID 23035077. The appointment as a Boston University School of Medicine research fellow will be for at least 1 year with possibility for extension based on performance. Applicants should have a strong background or interest in computational neuroscience and have a keen interest in interdisciplinary approaches that integrate modeling and empirical data in neuroscience research. Review of applications will begin immediately and will continue until the position is filled. Interested applicants should attach the following: - A cover letter, - A current CV, - A brief statement of current and future research interests, - The contact information of three references. Please be aware that references may be contacted anytime after receipt of your application. *Requirements:* - PhD or equivalent in computational neuroscience, applied mathematics, or a related field from an accredited institution is *required. * - Experience with NEURON compartmental modeling software and/or MATLAB scientific computing software is *required.* - Experience with differential equations-based mathematical models is *required.* - Excellent written and verbal communication skills is *required*. - Experience with conductance-based modeling of single neurons and/or excitatory-inhibitory networks is *preferred.* Please send inquiries and application materials to Dr. Christina Weaver, christina.weaver(a)fandm.edu . Christina M. Weaver, Ph.D. Department Chair, Mathematics Associate Professor Franklin & Marshall College P.O. Box 3003 Lancaster, PA 17604-3003 Email: christina.weaver(a)fandm.edu

Jan. 14, 2021