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Tutorials on Allen Institute data and tools for computational neuroscience at CNS*2021

by Anton Arkhipov

Dear all, Please join us for pre-CNS*2021 tutorials on June 30 and July 1: “From synapses to behavior – using open data, tools, and models from the Allen Institute in computational neuroscience”. https://www.cnsorg.org/cns-2021-tutorials#SA5 The Allen Institute recently released multiple free resources focusing on the structure and function of brain circuits, including data, associated analysis software, and models integrating the data to enable bio-realistic simulations. We will introduce several of these resources in a series of 1-hour sessions. The resources covered will include characterization of cell types and synapse types, 2-photon calcium imaging and Neuropixels electrophysiology in vivo, a visual behavior dataset, and bio-realistic models and modeling software. Wednesday, June 30, 2021 11:30 am – 11:45 am EST (8:30 am – 8:45 am PST) - Introduction 11:45 am – 12:45 pm EST (8:45 am – 9:45 am PST) - Synaptic Physiology (Luke Campagnola) 12:45 pm – 1:00 pm EST (9:45 am – 10:00 am PST) - Break 1:00 pm – 2:00 pm EST (10:00 am – 11:00 am PST) - Visual Coding 2-photon (Saskia de Vries) 2:00 pm – 3:00 pm EST (11:00 am – 12:00 pm PST) - Visual Coding Neuropixels (Josh Siegle) Thursday, July 1, 2021 11:30 am – 11:45 am EST (8:30 am – 8:45 am PST) - Introduction 11:45 am – 12:45 pm EST (8:45 am – 9:45 am PST) - PatchSeq (Nathan Gouwens) 12:45 pm – 1:00 pm EST (9:45 am – 10:00 am PST) - Break 1:00 pm – 2:00 pm EST (10:00 am – 11:00 am PST) - Visual Behavior (Alex Piet) 2:00 pm – 3:00 pm EST (11:00 am – 12:00 pm PST) - Bio-realistic model of the mouse primary visual cortex (Anton Arkhipov and Kael Dai) Please register for CNS*2021 and join us for the tutorials! https://www.cnsorg.org/cns-2021-quick Best wishes, Anton. Anton Arkhipov Associate Investigator T: 206.548.8414 E: antona(a)alleninstitute.org<mailto:antona@alleninstitute.org> [Text Description automatically generated] alleninstitute.org<https://alleninstitute.org> brain-map.org

June 23, 2021

Software WG satellite tutorials at CNS*2021 on Bash, Git, and Python: June 28, 29 2021

by Ankur Sinha

Dear all, Apologies for the cross-posts. The INCF/OCNS Software Working Group is running three beginner/intermediate level satellite tutorials on Bash, Git, and Python at CNS*2021. These tutorials are on Monday and Tuesday (28/29 June). They are intended for both complete beginners and occasional/regular users who are looking to expand and refresh their skills. More information on these, including topics that we will cover can be seen on our website: https://ocns.github.io/SoftwareWG/2021/06/09/software-wg-tutorials-at-cns-2… - Effective use of Bash (Felix B. Kern): 28 June, 2021 1200 UTC - Effective use of Git (Ankur Sinha): June 28, 2021 1700 UTC - Python for beginners (Joe Graham, Shailesh Appukuttan, Ankur Sinha): 29 June, 2021 1300 UTC One can register for CNS*2021 here to gain access to excellent set of tutorials/workshops/posters and oral presentations that are being organised this year: https://www.cnsorg.org/cns-2021 More information on the Software working group, our work, how you can contact us, and how you can join us (it is open to all) is here: https://ocns.github.io/SoftwareWG/index.html 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

June 23, 2021

Post-doc position on machine learning and human motion/physiological data analysis at AIST, Japan

by 平山淳一郎

Dear colleagues, We invite applications for a postdoctoral researcher position on machine learning and human motion/physiological data analysis, available at Mathematical Neuroscience Research Group, Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) (https://www.aist.go.jp/index_en.html) Japan. The successful candidate will join a collaborative project with ATR, Kyoto University and Hokkaido University on human-AI co-evolution, funded by NEDO (https://www.nedo.go.jp/english/) and conduct research on machine learning modeling and analysis of human motion data and/or related physiological signals from the brain and body, depending on his/her interests. The starting date is negotiable, with a preference for candidates who can start early. The initial appointment will be until March 2022, with the possibility of extension until March 31, 2025. Salary for the postdoctoral fellow will follow the AIST guideline. To apply, please visit https://jrecin.jst.go.jp/seek/SeekJorDetail?fn=3&ln=1&id=D121020014&ln_jor=1 and send the required application documents to junichiro.hirayama(a)aist.go.jp. The deadline of application is August 31, 2021. The deadline may be extended until the position is filled. -- Jun-ichiro Hirayama Senior Researcher Human Informatics and Interaction Research Institute National Institute of Advanced Industrial Science and Technology (AIST) junichiro.hirayama(a)aist.go.jp https://staff.aist.go.jp/junichiro.hirayama

June 23, 2021

Postdoctoral positions in the Geffen lab at the University of Pennsylvania

by Maria Geffen

The Geffen laboratory <http://hosting.med.upenn.edu/hearing> at the University of Pennsylvania <http://www.upenn.edu/> has multiple postdoctoral positions open in systems neuroscience with the broad goal of understanding the neuronal circuits for auditory perception and learning. We are looking for energetic and talented scientists interested in studying the function of the brain. The postdoctoral fellow will have the opportunity to learn and apply a host of systems neuroscience techniques, including two-photon imaging of population activity, optogenetic manipulations, large-scale electrophysiology and behavior in mice. Prior experience with some of these methods is preferred, but not required. Depending on the candidate’s interests, all projects provide an opportunity to learn and apply advanced computational methods, including dynamic systems analysis of neuronal population activity; Bayesian approaches for understanding the relation between neuronal activity and behavior; machine learning methods to understand large-scale neuronal activity. We currently have openings for postdoctoral fellows for three projects: (1) Neuronal mechanisms for predictive coding: Auditory perception relies on predicting statistics of incoming signals, be it identifying the speech of a conversation partner in a crowded room or recognizing the sound of a babbling brook in a forest. The human brain detects statistical regularities in sounds as a fundamental aspect of prediction, evidenced by reduced responses to repeated sound patterns and enhanced responses to unexpected sounds. Multiple studies demonstrate that the neuronal responses to regular signals are reduced through adaptation, which can contribute to prediction. However, adaptation alone is not sufficient to account for prediction and studies at cellular and neuronal population levels in animals thus far lend only partial support to existing theories of predictive coding. The goal of the project is to close this gap in knowledge and to determine the circuits that predict signals and detect statistical regularity and its violation in auditory behavior. Funded by NIH NIDCD. (2) Neuronal circuits for learning-driven changes in auditory perception: Everyday auditory behavior depends critically on learning-driven changes in auditory perception that rely on neuronal plasticity within the auditory pathway. By combining state-of-the-art optogenetic, electrophysiological, behavioral and computational approaches, the project seeks to identify the function of specific circuit elements in auditory learning. Funded by NIH NIDCD. (3) Neuronal mechanisms for hearing under uncertainty: In everyday life, because both sensory signals and neuronal responses are noisy, important cognitive tasks, such as auditory categorization, are based on uncertain information. To overcome this limitation, listeners incorporate other types of signals, such as the statistics of sounds over short and long time scales and signals from other sensory modalities into their categorization decision processes. This project will identify the contribution of specific cell types to categorization and the neuronal mechanisms for how contextual signals bias auditory categorization. In collaboration with Dr. Yale Cohen <https://auditoryresearchlaboratory.weebly.com/> and Dr. Konrad Kording <http://kordinglab.com/>, funded by NIH BRAIN Initiative. Our laboratory is a close community of fun-loving scientists, striving to help each other while exploring the mysteries of the brain. Our trainees have won numerous awards and have been awarded government and private foundation grants. We value diversity and promote equity in the scientific community and beyond <https://hosting.med.upenn.edu/hearing/philosophy/>. The systems neuroscience community at the University of Pennsylvania is top-notch and highly collaborative, and postdoctoral fellows will have opportunities to engage in interdepartmental initiatives, including MindCore <https://mindcore.sas.upenn.edu/>, MINS <https://www.med.upenn.edu/ins/> and CNI <https://www.cni.upenn.edu/>. Penn has a gorgeous campus and offers many cultural activities. Philadelphia is a beautiful city with world-class music, food and entertainment. To apply, please email Dr. Geffen at mgeffen(a)pennmedicine.upenn.edu <mailto:mgeffen@pennmedicine.upenn.edu> : a cover letter (summarize your prior research experience, why you are interested in the position, and your future plans) and your CV. __________________________ Maria N. Geffen, Ph.D. (she/her) Associate Professor Department of Otorhinolaryngology Department of Neuroscience Department of Neurology Stemmler Hall G14 3450 Hamilton Walk Philadelphia PA 19104 (215)898-0782 mgeffen(a)pennmedicine.upenn.edu http://hosting.med.upenn.edu/hearing Twitter: @neimarkgeffen

June 22, 2021

Three Assistant Professor Positions at University of Sussex

by Thomas Nowotny

Dear all, The School of Engineering and Informatics at the University of Sussex is seeking to hire three Assistant Professors (“Lecturers”, permanent position) in Computer Science and AI. One of the positions is particularly focused on a researcher with interests in one or more of the following areas: machine learning, ethical AI, computational Neuroscience, complexity science, consciousness science and bio-inspired AI and robotic control. They should be able to teach general subjects in Computer Science and Artificial Intelligence at Undergraduate and Taught Postgraduate levels. They will work within the Artificial Intelligence Research Group, including opportunities to interact with the robotics group in the Department of Engineering. The AI Research Group at the University of Sussex was created through the merger of the Evolutionary and Adaptive Systems (EASy) and the Data Science groups. We conduct research and teach a wide range of AI related topics, often cross-disciplinary and with a unique Sussex angle. We collaborate internationally and locally with academics, businesses, and public stakeholders, working at the frontiers of knowledge, on solving real-world problems, and in policy and public outreach. Applications should be accompanied by a full CV, and statements of future research plans and ways in which the applicant could contribute to teaching across the School. Please contact Dr Ian Mackie I.Mackie(a)sussex.ac.uk<mailto:I.Mackie@sussex.ac.uk> , Head of the Department of Informatics, for informal enquiries. The full job advert is posted at https://t.co/K0CdIYx6xH?amp=1 including a detailed person specification and details how to apply. Please get in touch if you are interested in these positions and forward to any interested colleagues. Kind regards, Thomas -- Prof Thomas Nowotny Head of the AI Research Group Director of Research and Knowledge Exchange School of Engineering and Informatics University of Sussex Falmer, Brighton BN1 9QJ, UK Phone: +44-1273-678593 FAX: +44-1273-877873

June 22, 2021

Post-doc / research associate position in neural reinforcement learning using causal models (Sheffield, UK, 33 months, deadline 4th July)

by Aditya Gilra

Dear All, We're looking for a post-doc / research associate to work on bio-plausible neural networks that learn causal models of the environment and utilize these to plan and explain actions in reinforcement learning. The position is for 33 months at the University of Sheffield, UK. Read more at: https://www.chistera.eu/projects/causalxrl . Apply via (deadline: 4th July): https://jobs.shef.ac.uk/sap/bc/webdynpro/sap/hrrcf_a_posting_apply?PARAM=cG… Best, Aditya. -- Aditya Gilra, Lecturer (Assistant Professor), Machine Learning Group <https://www.sheffield.ac.uk/dcs/research/groups/machine-learning> & Neuroscience Institute <https://www.sheffield.ac.uk/neuroscience-institute/research/computational-a…> , Department of Computer Science, University of Sheffield, UK. https://www.sheffield.ac.uk/dcs/people/academic/aditya-gilra

June 22, 2021

WWNeuRise series on neuromodulation & applications/recommendations

by William Podlaski

WorldWideNeuRise will host several online talks throughout June-July on the topic of neuromodulation in the brain from the following speakers: Wednesday, 30 June, 5pm CET Lindsay Collins (McCormick Lab, University of Oregon, USA) Cristina Colangelo (Blue Brain Project, EPFL, Switzerland) Wednesday, 14 July, 5pm CET Jasmine Pickford (Apps Lab, University of Bristol, UK) Luke Coddington (Dudman Lab, Janelia Research Campus, USA) Wednesday, 28 July, 5pm CET Rohan Sharma (Suhita Lab, IISER Pune, India) Ines Guerreiro (Gutkin Lab, Ecole Normale Superieure, France) For more information, please visit our website (https://neurise.github.io/) find us on WorldWideNeuro (https://www.world-wide.org/Neuro/WWNeuRise/) or follow us on Twitter (https://twitter.com/WWNeuRise) We are actively searching for PhD students and postdocs to give talks in our upcoming seminar blocks. On our website (https://neurise.github.io/) you can find an application form to directly apply, as well as a recommendation form, where you can suggest individuals from your lab, institute, or otherwise who you think might have an interesting story to tell! We are looking forward to seeing you at our upcoming seminars! The organising committee, Ellen Boven (Apps lab, University of Bristol) Christina Buetfering (Häusser lab, University College London) Lucie Descamps (Kentros lab, Norwegian University of Science and Technology) Gily Ginosar (Ulanovsky lab, Weizmann Institute) Loreen Hertäg (Clopath lab, Imperial College London) Joram Keijser (Sprekeler lab, TU Berlin) Bill Podlaski (Machens lab, Champalimaud Research)

June 21, 2021

NeuroML hands-on satellite tutorial at CNS*2021 on July 2nd 2021 at 1500 UTC

by Ankur Sinha

Dear all, Apologies for the cross-posts. We will be running a half day satellite tutorial at the 30th annual meeting of the Organization for Computational Neurosciences (OCNS), CNS*2021 Online. The tutorial will be held on July 2nd, 2021 at 1500 UTC. https://docs.neuroml.org/Events/202107-CNS2021.html The goal of the tutorial is to teach users to build, visualise, analyse, and simulate models using NeuroML. Why take part? --------------- This tutorial is aimed at new and current NeuroML users. We will start with a quick introduction to the NeuroML standard and the associated software ecosystem, after which we will proceed to conduct hands-on sessions to show how one can build computational models with NeuroML. Times and dates ---------------- - Friday 2nd July 1500 UTC Click here for your local time: https://www.timeanddate.com/worldclock/fixedtime.html?msg=NeuroML+tutorial+… Registration ------------- To take part in the tutorial, please register here for the CNS*2021 meeting: https://www.cnsorg.org/cns-2021 Pre-requisites --------------- The sessions will make use of the NeuroML Python tools. Please follow the documentation to install them on your system if you wish to use them locally: - PyNeuroML: https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html#pyneuroml - libNeuroML: https://docs.neuroml.org/Userdocs/Software/libNeuroML.html#libneuroml You can also use the interactive Jupyter notebooks from the documentation if you prefer (example: https://docs.neuroml.org/Userdocs/NML2_examples/SingleNeuron.html) These can be run on Binder and Google Collab in your web browser and do not require you to install anything locally on your computer. Slack ----- To aid communication with the community during (and after) the meeting, we have a Slack channel for NeuroML related discussions. Please contact Padraig Gleeson (p DOT gleeson AT ucl DOT ac DOT uk) or Ankur Sinha (ankur DOT sinha AT ucl DOT ac DOT uk) for an invite. You can also contact the NeuroML community using one of our other channels: https://docs.neuroml.org/NeuroMLOrg/CommunicationChannels.html#contact-chat We look forward to working with the community to drive further uptake of NeuroML compliant models and tools! -- 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

June 21, 2021

Q&A about INCF activities and membership

by Helena Ledmyr

Hello! Are you an open neuroscience practitioner or want to become one? Do you want to have input on global strategies for data sharing in neuroscience? Join the INCF network! INCF directors Helena Ledmyr and Mathew Birdsall Abrams will answer all your questions about INCF participation in our webinar on June 29th at 10am EDT / 4pm CEST, where long-time community member Samir Das (McGill U) will reflect on how he has benefited from membership. Register at bit.ly/INCFwebinar Information about INCF and memberships can be found on our website <https://www.incf.org/>. All the best, Helena Ledmyr ----------------------------- Helena Ledmyr, PhD *Director* *Development and Communications* International Neuroinformatics Coordinating Facility Secretariat Karolinska Institutet. Nobels väg 15A, SE-171 77 Stockholm. Sweden Email: helena.ledmyr(a)incf.org Phone: +46 8 524 870 35 incf.org neuroinformatics.incf.org

June 21, 2021

Assistant professor position in Göttingen, Germany

by Ecker, Alexander

We have an opening for an assistant professor position for ML/CV for biomedical applications in the computer science department at the University of Göttingen, Germany. Application deadline it July 11. For details see below or at https://www.uni-goettingen.de/en/645470.html The Faculty of Mathematics and Computer Science at the Georg-August-University of Goettingen invites applications for a Sartorius AG Endowed Junior Professorship W1 – „Computational Cell Analytics“ (all genders welcome) The junior professorship will be part of the "CIDAS-Sartorius lab for AI-based high-throughput analysis of cell systems" and will actively contribute to its further development. In the CIDAS-Sartorius Lab, we will develop novel data analysis methods to obtain scientific insights from observations of cell systems in various areas of the life sciences. It is a collaboration between the Campus Institute Data Science (CIDAS), the Institute for Computer Science, the University Medical Center Goettingen and Sartorius AG. The junior professorship will also be part of the Campus Institute Data Science (CIDAS) and contribute to its development. CIDAS is a central institution of the University of Goettingen and works closely with the partners of the Goettingen Campus such as the University Medical Center, several Max Planck Institutes, the German Primate Center, the Academy of Sciences and the German Aerospace Center Goettingen. The junior professorship is thus optimally integrated into Goettingen's top-notch life science research environment. The future holder of the position should have expertise in computer science with a focus on machine learning/deep learning and/or computer vision. The professorship contributes to the development of new analytical methods and their application in the field of cell analysis. Possible research foci are among others: - Computer vision in biomedical imaging - Biomedical image processing - Image based cell and biomolecular analytics - Methods for object recognition and image segmentation - Large-scale machine learning & deep learning - Nonlinear and dynamic prognosis models for the description and prediction of complex, nonlinear processes in cell models The candidate should have a track record of internationally competitive high-quality research and a high potential for groundbreaking research in internationally visible projects. The candidate is expected to contribute to teaching in the data science programs. Goettingen University is committed to research-oriented teaching. Applications of international scientists are highly encouraged. The University is an equal opportunity and family friendly employer. We specifically encourage women to apply. Disabled persons with appropriate qualifications and aptitude for the position will be given special consideration. Applications including CV, publications list and details of teaching and research including funded research projects should be submitted by 11 July 2021 online via the application portal: https://tinyurl.com/44r336yn For further information please contact Prof. Dr. Alexander Ecker, Institute of Computer Science and Campus Institute Data Science: ecker(a)cs.uni-goettingen.de. -- Alexander Ecker Professor of Data Science Department of Computer Science • Campus Institute Data Science University of Göttingen • Max Planck Inst. for Dynamics and Self-Organization Goldschmidtstr. 1 • room 2.137 • 37077 Göttingen https://eckerlab.org • @alxecker • +49 551 39-21272

June 21, 2021