- Comp-neuro - lists.cnsorg.org

Postdoctoral Fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience
by Paolo Avesani March 7, 2022

March 7, 2022

A postdoctoral fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience We are pleased to announce the opening of one Postdoctoral Fellowship at the Neuroinformatics Lab, an interdisciplinary initiative between the Center for Mind/Brain Sciences (CIMeC) of the University of Trento, and the Center for Digital Health of Fondazione Bruno Kessler. The position is part of the “Neusurplan” project, an integrated approach to neurosurgery planning based on multimodal and longitudinal data. The goal is to pursue an integrated approach to pre-operative neurosurgical planning, combining structural and functional characterization of brain connectivity. The data driven strategy will take advantage of a unique dataset of intra-operative points of directed electrical stimulation and the related functional responses. In this project, the candidate will pursue research on machine learning methods for neuroimaging data analysis to study and characterize brain connectivity, with applications to longitudinal studies and clinical practice. The ideal candidate should have a mixed background in neuroimaging techniques and numerate disciplines, like computer science, engineering, physics, or mathematics. This project is in collaboration with the Division of Neurosurgery, S. Chiara Hospital, Trento (IT). The position is for a 2 year Postdoc Fellowship (May, 2022 - April, 2024). To apply, follow the instructions at this link: https://bit.ly/nilab2022call Deadline for application: 21 March 2022. For questions about the position, please contact Paolo Avesani ( paolo.avesani(a)unitn.it) and/or Emanuele Olivetti (olivetti(a)fbk.eu) The University of Trento ranks among top Italian Universities ( https://www.unitn.it/en/ateneo/1636/rankings) Fondazione Bruno Kessler ranks first among the Italian research centers in Engineering and Computer Science ( https://magazine.fbk.eu/en/news/fbk-ranks-1st-in-italy-for-scientific-excel… ). To also consider a work/life balance, there is more than our passion for translational research. You can check these pointers for a flavor of life quality in Trentino: https://www.visittrentino.info/en; https://www.discovertrento.it/en A few papers related to the project are below: Bertò G,et al., (2021) Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation, Neuroimage, 224 https://doi.org/10.1016/j.neuroimage.2020.117402 Sarubbo S, et al., (2020) Mapping critical cortical hubs and white matter pathways by direct electrical stimulation: an original functional atlas of the human brain, Neuroimage, 205 https://doi.org/10.1016/j.neuroimage.2019.116237 Astolfi P, et al., (2020) Tractogram filtering of anatomically non-plausible fibers with geometric deep learning, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) LNCS, vol 12267. Springer https://doi.org/10.1007/978-3-030-59728-3_29 Sarubbo S, et al., (2021) Planning brain tumor resection using a probabilistic atlas of cortical and subcortical structures critical for functional processing: a proof of concept, Operative Neurosurgery, 20(3), 175-183 https://doi.org/10.1093/ons/opaa396 -- ------------------------------------------------------- Paolo Avesani Fondazione Bruno Kessler via Sommarive 18, 38050 Povo (TN) - I phone: +39 0461 314336 fax: +39 0461 302040 email: avesani(a)fbk.eu web: avesani.fbk.eu -- -- Le informazioni contenute nella presente comunicazione sono di natura privata e come tali sono da considerarsi riservate ed indirizzate esclusivamente ai destinatari indicati e per le finalità strettamente legate al relativo contenuto. Se avete ricevuto questo messaggio per errore, vi preghiamo di eliminarlo e di inviare una comunicazione all’indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material.

1 0

EMBO Practical Course - Barcelona summer school for Advanced Modelling of Behavior (BAMB!) -, September 1-8, 2022
by Alexandre Hyafil March 7, 2022

March 7, 2022

The Barcelona summer school for Advanced Modelling of Behavior (BAMB! <http://www.bambschool.org>) teaches advanced techniques in model-based analysis of behavior (humans and other species) to cognitive and computational neuroscientists at PhD and early career levels. This will be achieved through structured lectures, talks, hands-on tutorials and group projects aimed at making knowledge obtained directly applicable to the participants' own research. We want the trainees to acquire both the conceptual bases and the technical skills that will enable them to pursue a full modelling approach on their own when they come back to their lab. The course is intended for PhD students and postdocs in cognitive and computational neuroscience with a solid background in computational/quantitative analysis to benefit maximally from the advanced training offered by the course. Proficiency in either Python or Matlab is also required. We seek a nice blend of experimentalists (cognitive psychology / neuroscience) and theoreticians (with or without experience in cognitive modeling). Scientists from underrepresented groups and countries are especially encouraged to apply. The school is an EMBO Practical Course <https://www.embo.org/conferences-training/> and is organized by the Centre de Recerca Matemática <http://www.crm.cat>. A limited number of travel grants <https://www.embo.org/funding/lecture-travel-and-childcare-grants/travel-gra…> will be available from EMBO. Organizers: Chris Summerfield (Oxford / Deepmind) Klaus Wimmer (CRM, Barcelona) Alex Hyafil (CRM, Barcelona) Confirmed Faculty: Jean Daunizeau (ICM, Paris) Alex Hyafil (CRM, Barcelona) Máté Lengyel (Cambridge) Zhaoping Li (Tübingen) Alfonso Renart (Champalimaud) Marion Rouault (ENS Paris) Kim Stachenfeld (Deepmind) Chris Summerfield (Oxford / Deepmind) MH Tessler (Deepmind) Klaus Wimmer (CRM, Barcelona) Dates and location: September 1-8, downtown Barcelona, Spain Applications are open until April 13. Please see the course website for further details: www.bambschool.org.

1 0

INCF/OCNS Software working group survey on software usage
by Ankur Sinha March 7, 2022

March 7, 2022

Dear all, We, the INCF/OCNS Software working group, are conducting a short anonymous survey to collect information on the usage of common software tools in comp-neuro. Could we please request you to spend 2 minutes of your time to fill it out here: https://forms.gle/NXWv2CwtWBSB9BXv9 The information gathered in the survey will be used to organise sessions/workshops related to the software, and improve awareness about them and their maintenance. On behalf of the Software WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

1 0

Survey on the technical landscape and barriers present in EEG research informatics
by Christian O'Reilly March 6, 2022

March 6, 2022

Dear colleagues, We'd appreciate your time completing this brief survey, for a new initiative, EEGNet <https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-4544555345…> , which aims to leverage open-source infrastructure for sharing and annotating open standardized EEG datasets with automated processing workflows. We are keen to have your views on the technical landscape and barriers present in EEG research informatics. Click here to take this survey <https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-4544555345…> (https://tinyurl.com/4rruuz42) which should take around 10 minutes -- and thank you for sharing it with colleagues in your field. If you're interested in sharing tools and data through EEGNet and providing more input on the platform, please let us know via the embedded links you'll find in the survey. EEGNet is a constituent organization of the Global Brain Consortium (GBC <https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-4544555345…>), an international neuroscience collaboration focused on EEG-mediated applications in global health. Thank you for your valuable input - We are hoping to have all responses back as soon as possible. Christian O'Reilly ------------------ Assistant Professor, University of South Carolina (UofSC) Department of Computer Science and Engineering Artificial Intelligence Institute (#AIISC) Autism and Neurodevelopmental Disorders Center (#USCAND) Institute for Mind and Brain

1 0

Postdoc position
by Cian O'Donnell March 4, 2022

March 4, 2022

Postdoc position in Computational Neuroscience Intelligent Systems Research Centre, Ulster University, Derry/Londonderry, UK We are looking for a computational/mathematical neuroscience research associate to build stochastic models of gene expression in neurons to try to understand how or if synapses can store information stably. Post has funding for up to 3 years. You will be based in the group of Cian O'Donnell at Ulster University in Derry, Northern Ireland, UK (https://odonnellgroup.github.io) but closely collaborating with and visiting the mathematical neuroscience group of Romain Veltz at INRIA, Sophia-Antipolis, France (http://romainveltz.pythonanywhere.com) In addition to mathematical/computational modelling, as part of the project you will have the opportunity to analyse in vivo and in vitro imaging data from experimental collaborators Noam Ziv, Technion, Israel (https://noamziv.net.technion.ac.il) and Haining Zhong, OHSU, USA (https://www.hainingzhonglab.com) You will also be a member of the Intelligent Systems Research Centre (http://isrc.ulster.ac.uk) which hosts a community of researchers working across computational and cognitive neuroscience, neurotechnology, neuromorphic engineering, machine learning, robotics and related fields. You should have: - PhD in computational neuroscience/biology, applied mathematics, computer science, engineering, physics, or related field. - Expertise in one or more programming languages for scientific computing such as Python, Julia, MATLAB, or similar. - Experience of computational/mathematical modelling of biological or related systems. Derry is lively city of ~100K people situated on the River Foyle, in the north-west of the island of Ireland. It has a highly affordable cost of living, thriving cultural scene, and access to spectacular coastal scenery and the great outdoors in Donegal and the north coast of Northern Ireland. Application deadline is 13th March 2022. Follow this link (https://www.ulster.ac.uk/about/jobs) and search for job ref 010982. Please contact Cian (c.odonnell2(a)ulster.ac.uk<mailto:c.odonnell2@ulster.ac.uk>) for informal enquiries. -- Cian O’Donnell Lecturer in Data Analytics School of Computing, Engineering and Intelligent Systems Ulster University https://odonnellgroup.github.io

1 0

Postdoc in Computational Neuroscience at NYU
by Cristina Savin Feb. 28, 2022

Feb. 28, 2022

Postdoc in Computational Neuroscience at NYU We are seeking a creative and driven computational neuroscience postdoctoral fellow to work on a collaborative project between the labs of Dora Angelaki (https://angelakilabnyu.org/ <https://angelakilabnyu.org/>) and Cristina Savin (http://www.cns.nyu.edu/~csavin <http://www.cns.nyu.edu/~csavin>) at New York University. The project studies neural representations underlying foraging behavior in monkeys, comparing both freely-moving and head-restrained behaviors, funded by the NIH BRAIN Initiative. The position is initially for one year, with the possibility of renewal. The successful candidate will have: a strong quantitative background demonstrable interest in neuroscience obtained (or be close to the completion of) a PhD in computational neuroscience, physics, mathematics, computer science, machine learning, statistics, etc ability to work in a strongly collaborative and interdisciplinary setting Preference will be given to candidates with: expertise in probabilistic machine learning strong programming skills, ideally in python previous experience with neural data analysis To send your application please provide your cv, a brief statement of research interests, and the contact details for reference letters to <csavin(a)nyu.edu <mailto:csavin@nyu.edu>>. For informal queries, please contact Cristina Savin (csavin(a)nyu.edu <mailto:csavin@nyu.edu>) or Dora Angelaki(da93(a)nyu.edu <mailto:da93@nyu.edu>). We will be available for in person discussions at the upcoming Cosyne meeting.

1 0

Assistant Professor in Computational Neuroscience (W1) with tenure track option (to W2) at the Institute for Cognitive Science, University of Osnabrück.
by Peter König Feb. 28, 2022

Feb. 28, 2022

Great opportunity in Computational Neuroscience: Assistant Professor in Computational Neuroscience (W1) with tenure track option (to W2) at the Institute for Cognitive Science, University of Osnabrück. (apologies for multiple postings) Full details at: https://www.uni-osnabrueck.de/universitaet/stellenangebote/stellenangebote-… --- This tenure-track Professorship is funded by the German Federal Government and the Länder under its Program for the Promotion of Young Academics (Tenure-Track Program). Upon meeting the general administrative requirements, you will be employed as a civil servant on limited tenure for an initial period of three years. If you receive a positive evaluation after the initial three years, this period can be extended by up to three further years. If you meet Osnabrück University’s standards with respect to ability, competence and academic achievement, you will be offered a tenured W2 Professorship in accordance with the relevant legal provisions without further application. Tasks and Responsibilities: Research and teaching should be in the area of computational neuroscience. The professorship and research should be focused on understanding principles of neuronal information processing and cognitive processes. The professorship complements and cooperates with the existing research groups of the Institute of Cognitive Science at Osnabrück University. Further, the holder of the position should actively contribute to existing and future collaborative research projects (e.g. RTG Situated Cognition, RTG Computational Cognition) and should participate in the respective continuation research proposal of the Research Training Group Computational Cognition. In addition, the professorship should engage in teaching in all degree programs of Cognitive Science (BSc, MSc, PhD). Teaching is in English. Conditions of Employment: Condition of employment is: - Research experience in the field of neuronal information processing with the focus of understanding principles of neuronal information processing or cognitive processes. - Research focus on at least one of the two following topics: - Methods of Experimental cognitive neuroscience like EEG, MEG, fMRI, TMS, cell recordings, eyetracking, or virtual reality - Models of information processing in neurons, networks of neurons like for example deep neuronal networks and machine learning. - A coherent research profile, must be motivated by or explain experimental data and there must be a realistic perspective to implement all parts of the own research, including the experimental components or data collection, at the university of Osnabrück. - An excellent command of the English language. - Willingness to participate in university administrative processes and commission work. For non-German speaking applicants, willingness is expected to learn the German language with a sufficient proficiency within two years. In addition, it would be welcome: - Teaching experience in the field of the professorship - Experience with acquiring third party research funding. Legal Conditions of Employment: You will hold a first degree, have a strong commitment to teaching, and have demonstrated your ability to engage independently in advanced academic research, as a rule by obtaining an outstanding PhD (in accordance with Section 30 subsection 2 of the Lower Saxony Higher Education Act [NHG]) in a relevant subject. The time between the applicant’s final PhD examination or the completion of other equivalent qualifications which qualify the applicant for the position in accordance with Section 30 para. 2 sentence 1 No. 3 Lower Saxony Higher Education Act and the applicant’s application for the assistant professorship should be no longer than four years. This period of time does not include periods caring for a child or several children under 18 years of age or periods caring for a dependent relative and increases by up to two years per child or period of care to a maximum four years in multiple cases of care (Section 30 para. 5 Lower Saxony Higher Education Act). The position is available on a full-time or part-time basis. Osnabrück University is a family-friendly university and is committed to helping working/studying parents balance their family and working lives. Osnabrück University is actively seeking to increase the number of female Professors in its employ. Applications from women are therefore particularly welcome. If two candidates are equally qualified, preference will be given to the candidate with disability status. For further information, please contact Prof. Dr Gordon Pipa, Tel. +49 541-969-2277, E-Mail: gpipa(a)uni-osnabrueck.de. Please submit your application (including a resume with full details of your scholarly and scientific employment history, list of publications and courses taught as well as planned research) in electronic form (as one pdf file) together with the “Bewerbungsprofil” [“Applicant Profile”] (DOCX, 13,58 kB) to the Dean of the School of Human Sciences, Prof. Dr. Susanne Boshammer, Universität Osnabrück, 49069 Osnabrück (bewerbungfb08(a)uni-osnabrueck.de) to arrive by March 27, 2022. Please enter the code word "CNtt" in the subject of your e-mail. We look forward to receiving your application. -- Prof. Dr. Peter König, Institute of Cognitive Science, University Osnabrück

1 0

Assistant Prof (W1) TT @ Uni Osnabrück, Germany
by Ulrich G. Hofmann Feb. 25, 2022

Feb. 25, 2022

This open position may be of interest to Comp Neuro scientists: https://www.uni-osnabrueck.de/universitaet/stellenangebote/stellenangebote-… ulrich hofmann

1 0

Announcing Okinawa/OIST Computational Neuroscience Course 2022
by Erik De Schutter Feb. 25, 2022

Feb. 25, 2022

OKINAWA/OIST COMPUTATIONAL NEUROSCIENCE COURSE 2022 Methods, Neurons, Networks and Behaviors June 13 to June 29, 2022 Okinawa Institute of Science and Technology Graduate University, Japan https://groups.oist.jp/ocnc After two consecutive cancelations due to COVID-19, OCNC 2022 will take place on June 13-29, preceding Neuro2022 (https://neuro2022.jnss.org) in Okinawa. Depending on the immigration situation in June the course will be either pure on-site or hybrid: a mixture of on-site and remote. The aim of the Okinawa/OIST Computational Neuroscience Course is to provide opportunities for young researchers with theoretical backgrounds to learn the latest advances in neuroscience, and for those with experimental backgrounds to have hands-on experience in computational modeling. We invite graduate students and postgraduate researchers to participate in the course, held from June June 13 through June 29, 2022 at an oceanfront seminar house of the Okinawa Institute of Science and Technology Graduate University. Applications are through the course web page (https://groups.oist.jp/ocnc) only: January 26 - February 28, 2022. Applicants will receive confirmation of acceptance in April. The 17th OCNC will be a shorter course than in the past: a two-week course covering single neurons, networks, and behaviors with time for student projects. Teaching will focus on methods with hands-on tutorials during the afternoons, and lectures by international experts. The course has a strong hands-on component based on student proposed modeling or data analysis projects, which are further refined with the help of a dedicated tutor. Applicants are required to propose their project at the time of application. However in the case of a hybrid format course, only on-site students will receive support for student projects. There is no tuition fee. The sponsor will provide lodging and meals during the course and may provide partial travel support. We hope that this course will be a good opportunity for theoretical and experimental neuroscientists to meet each other and to explore the attractive nature and culture of Okinawa, the southernmost island prefecture of Japan. Invited faculty: • Michael Berry II (Princeton University, USA) • Anne Churchland, Cold Spring Harbor Labs, USA • Erik De Schutter (OIST) • Kenji Doya (OIST) • Gaute Einevoll, Norwegian University of Life Sciences (online) • Tomoki Fukai (OIST) • Boris Gutkin (Ecole Normale Supérieure, Paris, France) • Yukiyasu Kamitani, Kyoto University, Japan • Bernd Kuhn (OIST) • Sang Wan Lee, KAIST, South Korea • Devika Narain, Erasmus Medical Center, Rotterdam, Netherlands • Viola Priesemann, MPG Göttingen, Germany (online) • Ivan Soltesz, Stanford University, USA • Greg Stuart, Australian National University, Australia • Greg Stephens (OIST) • Saori Tanaka, (ATR, Japan) • Marylka Yoe Uusisaari (OIST)

1 1

14ᵗʰ Advanced Scientific Programming in Python in Bilbao Spain, 5–11 September, 2022
by Jakob Jordan Feb. 23, 2022

Feb. 23, 2022

ASPP2022: 14ᵗʰ Advanced Scientific Programming in Python ======================================================== a Summer School by the ASPP faculty and the Faculty of Engineering of the Mondragon University, Bilbao https://aspp.school Scientists spend more and more time writing, maintaining, and debugging software. While techniques for doing this efficiently have evolved, only few scientists have been trained to use them. As a result, instead of doing their research, they spend far too much time writing deficient code and reinventing the wheel. In this course we will present a selection of advanced programming techniques and best practices which are standard in the industry, but especially tailored to the needs of a programming scientist. Lectures are devised to be interactive and to give the students enough time to acquire direct hands-on experience with the materials. Students will work in pairs throughout the school and will team up to practice the newly learned skills in a real programming project — an entertaining computer game. We use the Python programming language for the entire course. Python works as a simple programming language for beginners, but more importantly, it also works great in scientific simulations and data analysis. We show how clean language design, ease of extensibility, and the great wealth of open source libraries for scientific computing and data visualization are driving Python to become a standard tool for the programming scientist. This school is targeted at Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or R is absolutely required. Basic knowledge of Python and of a version control system such as git, subversion, mercurial, or bazaar is assumed. Participants without any prior experience with Python and/or git should work through the proposed introductory material before the course. We are striving hard to get a pool of students which is international and gender-balanced. Date & Location =============== 5–11 September, 2022. Bilbao, Spain. Application =========== You can apply online: https://aspp.school Application deadline: 23:59 UTC, Sunday 1 May, 2022. There will be no deadline extension, so be sure to apply on time. Be sure to read the FAQ before applying: https://aspp.school/wiki/faq Participation is for free, i.e. no fee is charged! Participants however should take care of travel, living, and accommodation expenses by themselves. We are in the process of securing some funds for supporting students with accommodation and living costs. Program ======= • Version control with git and how to contribute to open source projects with GitHub • Best practices in data visualization • Testing and debugging scientific code • Advanced NumPy • Organizing, documenting, and distributing scientific code • Advanced scientific Python: context managers and generators • Writing parallel applications in Python • Profiling and speeding up scientific code with Cython and numba • Programming in teams Faculty ======= • Jakob Jordan, Department of Physiology, University of Bern Switzerland • Jenni Rinker, Department of Wind Energy, Technical University of Denmark, Roskilde Denmark • Lisa Schwetlick, Experimental and Biological Psychology, Universität Potsdam Germany • Nicolas Rougier, Inria Bordeaux Sud-Ouest, Institute of Neurodegenerative Diseases, University of Bordeaux France • Pamela Hathway, GfK, Nuremberg Germany • Pietro Berkes, NAGRA Kudelski, Lausanne Switzerland • Rike-Benjamin Schuppner, Institute for Theoretical Biology, Humboldt-Universität zu Berlin Germany • Tiziano Zito, Department of Psychology, Humboldt-Universität zu Berlin Germany • Zbigniew Jędrzejewski-Szmek, Red Hat Inc., Warsaw Poland Organizers ========== Head of the organization for ASPP and responsible for the scientific program: • Tiziano Zito, Department of Psychology, Humboldt-Universität zu Berlin Germany Organization team in Bilbao: • Aitor Morales-Gregorio, Theoretical Neuroanatomy, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Jülich, Germany • Carlos Cernuda, Data Analysis & Cybersecurity, Faculty of Engineering, Mondragon Unibertsitatea, Bilbao Spain Website: https://aspp.school Contact: info(a)aspp.school

1 0