October 2020 - Comp-neuro - lists.cnsorg.org

Scientist I position at the Allen Institute - Bio-realistic Modeling of Reconstructed Cortical Tissue

by Anton Arkhipov

Scientist I - Bio-realistic Modeling of Reconstructed Cortical Tissue https://alleninstitute.hrmdirect.com/employment/job-opening.php?req=1415274 Our mission at the Allen Institute is to advance our understanding of how the brain works in health and disease. Using a team science approach, we strive to discover how the brain implements fundamental computations through the integration of technological innovation, cutting-edge experiments, modeling, and theory. The Allen Institute is seeking exceptional candidates for a BRAIN Initiative-funded position of Scientist in our Seattle-based multidisciplinary organization. The Scientist will join the computational team of Anton Arkhipov and will focus on data analysis and modeling of structure, activity, and computations in mouse cortical circuits. This project will take advantage of unprecedented experimental datasets from the Allen Institute that contain a systematic characterization of synaptic connections between the cell types (https://portal.brain-map.org/explore/connectivity/synaptic-physiology) and a connectome of individual neurons coupled with dense recordings of activity in the mouse visual cortex (https://microns-explorer.org<https://microns-explorer.org/>). The Scientist will work collaboratively with colleagues to integrate these data into new, highly realistic network models of cortical circuits, use the models to explore theoretical predictions, and provide them as a resource to fuel future theoretical, modeling, and experimental work in the community. Our computational team collaborates closely with experimentalists to build systematic classifications of structure and function of the mouse visual cortex based on high-throughput recordings in vitro (e.g., Gouwens et al., Nature Neurosci., 2019; Gouwens et al., Cell, in press, 2020, https://doi.org/10.1101/2020.02.03.932244) and in vivo (e.g., Siegle et al., Nature, in press, 2020, https://doi.org/10.1101/805010) Using systematically constructed models of neurons from diverse types, we are building and simulating data-driven, highly realistic models of the mouse visual cortex (Arkhipov et al., PLOS Comp. Bio., 2018; Billeh et al., Neuron, 2020; https://portal.brain-map.org/explore/models) The team also develops and disseminates modeling software (https://alleninstitute.github.io/bmtk/; https://github.com/AllenInstitute/sonata) Join us to analyze world-class experimental data and build the next generation of brain models! Essential Functions * Collaborate with in-house experimentalists to analyze data from the synaptic physiology and 2-photon calcium imaging/electron microscopy connectomics datasets. * Use these data to build and simulate models of cortical circuits, in order to study mechanisms connecting circuit structure and function. * Publish/present findings in peer-reviewed journals/scientific conferences. Required Education and Experience * PhD degree in Neuroscience, Physics, Applied Mathematics, or related fields. * 0-2 years of post-doctoral experience. * Strong publication record. * Track record of scientific excellence and independent thinking. Preferred Education and Experience * Experience in computational neuroscience and/or systems neuroscience is preferred, but other strong applicants will be considered (with background in computational physics, biophysics, and related disciplines). * Candidates with strong background in experimental systems neuroscience, willing to switch to computational work, are encouraged to apply. * Experience with scientific programming (e.g., in Python) and sharing/collaborative development of software (e.g., GitHub) is a plus. Physical Demands * Fine motor movements in fingers/hands to operate computers and other office equipment; lab equipment Position Type/Expected Hours of Work * This role is currently able to work remotely due to COVID-19 and our focus on employee safety; this may change, and you may be required to work onsite at our South Lake Union office as safety restrictions are lifted in relation to COVID-19. It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities. Apply here: https://alleninstitute.hrmdirect.com/employment/job-opening.php?req=1415274

Oct. 27, 2020

New release of the Comp-Neuro Fedora Linux operating system for computational neuroscience is now available for download

by Ankur Sinha

Hello everyone, (Apologies for the cross posts) I am happy to announce that the latest release of the Comp-Neuro Fedora Linux based operating system for computational neuroscience research is now available for download from: https://labs.fedoraproject.org/comp-neuro/ For those that prefer torrents to direct server downloads, it can also be downloaded here: https://torrent.fedoraproject.org/ Detailed documentation can be accessed at: https://neuro.fedoraproject.org Based on the Fedora Workstation OS[1], the Comp-Neuro installer image includes a plethora of computational neuroscience software[2]. This includes: - commonly used simulators: NEST, NEURON, Brian2, Arbor, Auryn, CalC, COPASI, GENESIS, MOOSE; - the complete Python 3.9 science stack: Matplotlib, Jupyter notebooks, Numpy, Pandas, Pillow, Scikit-image, Scikit-learn, Scipy, Statsmodels, Sympy, *and* other utilities such as GNU Octave. Comp-Neuro Fedora also uses the popular and modern GNOME desktop environment[3], and so includes all the productivity tools that are part of the latest GNOME 3.38 release. Further, more software that is not included in the installation media can also be installed from the Fedora software repositories[4] and from FlatHub[5]. The ISO installer image is a "live" image, which means one can also run the operating system directly off the image without installing it to disk Fedora, and so Comp-Neuro Fedora is completely Free and Open Source Software, which is free for everyone to use, share, study, and modify. It is developed by the volunteer community driven NeuroFedora Special Interest Group (SIG). Any feedback and comments are most welcome[6]. If you develop software for neuroscience research, please consider getting in touch with the NeuroFedora community to help us include it in NeuroFedora. Everyone is welcome to join the community and work on whatever tasks they find interesting[7]. No prior knowledge or skills are expected. [1] https://getfedora.org/en/workstation/ [2] https://docs.fedoraproject.org/en-US/neurofedora/compneuro-tools/ [3] https://www.gnome.org/ [4] https://docs.fedoraproject.org/en-US/neurofedora/software/ [5] https://flathub.org/home [6] https://docs.fedoraproject.org/en-US/neurofedora/communicating/ [7] https://docs.fedoraproject.org/en-US/neurofedora/contributing/ On behalf of the NeuroFedora community, -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

Oct. 27, 2020

Job opportunity - Postdoctoral Sleep Researcher at Bitbrain (Zaragoza, Spain)

by Eduardo López-Larraz

We are looking for a postdoctoral sleep researcher to join Bitbrain <https://www.bitbrain.com/> and work on an EU-funded neurotechnology research project. The main objective will be to exploit some of the most recent advances in sleep research to develop interventions based on cutting-edge wearable neurotechnology for sleep (and sleep-mediated cognitive processes) improvement. The candidate will join Bitbrain <https://www.bitbrain.com/>’s interdisciplinary R&D department of applied neuroscience and neurotechnology and will lead all the R&D activities related to sleep. The candidate will have to: 1) design the R&D strategy of this new area in the company, which will require attending and participating in international events and networks, and 2) design and carry out a feasibility study in sleep improvement using innovative and practical technologies that can be used outside the lab. The position is initially offered for 12 months and includes a relocation and training package. *Requirements*: Sleep expert with a PhD degree in Neuroscience, Psychology, Biomedical Engineering or similar. Strong background in sleep research, understanding of EEG (required) and brain stimulation (desirable). Project management skills. Problem solving and potential of growth. English is required, Spanish is a plus. *We offer*: - Competitive salary. Benefits associated with mobility and family. - Possibility of doing part of the work remotely (to be discussed). - Work-life balance. * Starting date: *01.03.2021 *Application Deadline*: 15.12.2020 More information and application procedure: https://euraxess.ec.europa.eu/jobs/545040

Oct. 27, 2020

postdoc position with Christopher Rozell at Georgia Tech

by Christopher Rozell

A postdoctoral position in computational neuroscience is available in the lab of Christopher Rozell at the Georgia Institute of Technology (Atlanta, GA). This BRAIN Initiative research project seeks to advance the field of closed-loop computational neuroscience by pioneering the use of real-time feedback stimulation during experiments to decouple recurrently connected circuit elements and make stronger causal inferences about circuit interactions. This position will have a broad opportunity to develop models and algorithms that are implemented in novel experiments using closed-loop optogenetic stimulation. We aim to provide both new scientific insight about computation in neural circuits (especially sensory coding in the thalamo-cortical circuit) as well as new approaches and algorithmic tools for the community to use in novel electrophysiology experiments. This position will work as part of a team and in close collaboration with the experimental lab of Garrett Stanley (also at Georgia Tech), and it is expected that the computational and algorithmic approaches will be implemented experimentally through close partnership with experimentalists in the Stanley Laboratory. Applicants should hold a PhD in a related discipline with a strong record of research impact, quantitative thinking and collaborative work. Experience in computational neuroscience, machine learning, feedback control, and causal inference is all advantageous. The lab is committed to providing a diverse and inclusive environment for all scholars, and applications are especially encouraged from all underrepresented groups. Additionally, the lab is committed to the professional development of the members, making it valuable preparation for people who are interested in academic, industrial or entrepreneurial careers. The position has no mandatory teaching or administrative duties. Excellent (written and oral) communication skills in English are required. This particular project is part of the Collaborative Research in Computational Neuroscience program (CRCNS), providing access to a community of researchers across the country who are focused on similar types of collaborations between computational and experimental labs. Georgia Tech's campus in the heart of midtown Atlanta, which has a thriving and collaborative neuroscience community that has a particular emphasis on computational and systems neuroscience. Atlanta is also one of the fastest-growing metropolitan areas in the United States, boasting a wide range of opportunities for recreation and culture. Georgia Tech has competitive benefits (including comprehensive medical insurance) and is an equal opportunity employer. The position would ideally start as soon as possible (spring 2021). The appointment is initially for 12 months with the expectation of renewal. Compensation will be commensurate with relevant experience. Candidates should send a CV, a statement of research experience and interests, expected date of availability, and the contact information for three references to crozell(a)gatech.edu with the subject line "CRCNS postdoc". Application review will proceed until the position is filled and should be received by December 1 for full consideration.

Oct. 27, 2020

[virtual event] - neuromorphic colloquium

by Chiara Bartolozzi

The NEUROTECH Educational Team is organizing a webinar series on neuromorphic computing technologies. The objective is to offer educational material about the field but also hold discussions with the experts about how the field started, how it evolved, where it’s going and how it’s going to shape the future industrial landscape. The first webinar will be on the 3rd of November at 16 CET and the question of the day is: “What is Neuromorphic Engineering?”. The first speakers are: Prof. Giacomo Indiveri, Prof. Steven Furber, Prof. Bernabé Linares-Barranco and Prof. Kwabena Boahen. You can register for free here: https://neurotech.iniforum.ch/educational/ Join us and spread the word! This initiative is supported as part of the NEUROTECH EU-H2020 coordination and support action. ----------------------------------------------------------------------------------------------------------------------------------------- About Neurotech: Our mission is to catalyse research and collaboration in NCT. Today's neuromorphic community in Europe is leading the state of the art in this domain. The community counts an increasing number of labs that work on theory, modelling, and implementation of neuromorphic computing systems. The NEUROTECH Project will create a Cartography of NCT in Europe, explore Roadmaps for its development, collect educational and information resources on NCT, and inform about upcoming and previous events. https://neurotech.iniforum.ch Follow us on LinkedIN: NEUROTECHAI

Oct. 26, 2020

Postdoc position in Bologna

by Andrea Santamaria

Dear Sirs, We are the ERC Project INSCRIBE Invention of Scripts and their Beginnings. Sorry for having forget the title, which I've now included in the object as "Postdoc position in Bologna". We would therefore be delighted to share our announcement on your list. You can find the dame text here below in bold. The ERC Project INSCRIBE Invention of Scripts and their Beginnings, based at the University of Bologna, Italy, seeks candidates for a postdoctoral position in interdisciplinary research with expertise in computational neuroscience. The selected candidate will straddle the borders of neuroscience, cognition and the evolution of graphic codes, to apply quantitative methods to large databases with the goal of establishing commonalities worldwide in the evolution of symbols from a broadly cognitive, and more specifically, motor-driven and visual perspective. The ideal candidate will have earned a PhD in either neuroscience or neural computational sciences, with skills in statistical methods. The position is renewable on a yearly basis, up to three consecutive years and can be held remotely. Deadline: 28 October 2020. For more information on how to apply: https://site.unibo.it/inscribe/en/jobs or contact: s.ferrara(a)unibo.it. Thank you in advance and Kind Regards, Andrea Santamaria Get Outlook for Android<https://aka.ms/ghei36>

Oct. 26, 2020

Neuromatch conference Oct 26-30

by Goodman, Daniel F M

This is just a reminder that the Neuromatch conference starts tomorrow (at the time of writing) Oct 26-30. We have around 900 talks on all aspects of neuroscience, debates, panels, as well as special series in partnership with the BRAIN initiative, Black in Neuro, and Queer in Neuro. Check our our website here: https://www.neuromatch.io/ Registration is $25, but can be waived with the press of a button, no questions asked, if you're not able to pay. You can see the full agenda with recommendation engine once you've registered, or you can use our old fashioned schedule here before registering (but no automatic recommendations on this one): https://neural-reckoning.github.io/nmc3_provisional_schedule/ Please pass this message on to anyone or any list you think would be interested. Many thanks, The Neuromatch organisers

Oct. 25, 2020

Postdoc position on Biological Deep Learning

by Walter Senn

Dear all A second postdoc position devoted to learning in deep cortical networks is available in our Computational Neuroscience labs at the University of Bern, Switzerland. This position is focussed on formulating error-based learning in deep cortical networks in terms of a principle of least action. We will extend this theory to natural gradient learning and to learning with spiking neurons. The research of our labs is more broadly devoted to biologically realistic models of spatio-temporal processing in cortical networks and their relation to reinforcement learning, Bayesian computing, and neuromorphic implementations. The position is part of the European Human Brain Project and is available by January 1st, 2021, for 2 years (extendable). We offer a stimulating environment with three research groups in theoretical and computational neuroscience, along with experimental neuroscience at the same Department of Physiology (physio.unibe.ch/gruppen.aspx <http://physio.unibe.ch/gruppen.aspx>), as well as close collaborations with other labs in neuroscience, artificial intelligence and neuromorphic engineering. Ideal candidates should have a strong background in computational neuroscience, machine learning, applied mathematics and/or physics. Please send your CV, publication list, letter of motivation and contact information for at least two references to Walter Senn (walter.senn(a)unibe.ch <mailto:walter.senn@unibe.ch>) and Mihai Petrovici (mihai.petrovici(a)unibe.ch <mailto:mihai.petrovici@unibe.ch>), with cc to Virginie Sabado (virginie.sabado(a)unibe.ch <mailto:virginie.sabado@unibe.ch>). The first evaluation round will begin on November 8, 2020. The positions will remain open until filled. With best regards, Mihai Petrovici and Walter

Oct. 23, 2020

Postdoctoral position on the integration of vision and behaviour (Schröder Lab, University of Sussex, UK)

by Sylvia Schröder

The Schröder Lab <https://www.sussex.ac.uk/research/labs/schroeder-lab/>(Vision and Behaviour) at the University of Sussex, UK, offers a position for a *Postdoctoral researcher*** to study information processing in the early visual system of mice using two-photon imaging, electrophysiology (Neuropixels probes), and opto- and chemogenetic manipulations. The lab’s goal is to determine how behavioural and internal states like arousal are integrated with visual responses in the retina and superior colliculus. We want to discover the underlying mechanisms and the purpose of this integration in terms of visual processing and the animal’s behavioural demands. This paper describes our previous findings. *Your profile* ·Phd degree in neuroscience or in physics, computer science or engineering with a keen interest in neuroscience ·You will take ownership of the project and drive it forward ·Experience in experimental biology and quantitative data analysis including programming in Python, Matlab or a similar language ·Experience with two-photon imaging and/or extracellular electrophysiology desirable *Our offer to you* The Schröder lab opens its doors in January 2021. The candidate will have the opportunity: ·to make use of the lab’s own two-photon microscopy and Neuropixels recording setups ·to benefit from the PI’s active support in research and her mentoring in career development ·to learn essential skills in organising and setting up a lab ·to shape the research culture of the lab based on the values of scientific excellence, team work, and diversity ·to collaborate with other labs within Sussex Neuroscience <https://www.sussex.ac.uk/research/centres/sussex-neuroscience/>with expertise visual and other sensory systems, mouse behaviour, techniques of two-photon imaging and electrophysiology, and computational neuroscience *Start date*: January 2021 or later *Contract*: for 2 years initially, funding available for 5 years (through Sir Henry Dale Fellowship, Wellcome Trust) *Location*: campus is just outside Brighton at the coast of South East England, surrounded by South Downs National Park, 1 h from London See**the ***job advertisement <https://www.sussex.ac.uk/about/jobs/research-fellow-in-neuroscience-4726>* for details on how to apply. Informal enquiries are highly encouraged and should be made to Sylvia Schröder (sylvia.schroeder(a)ucl.ac.uk) **

Oct. 23, 2020

Postdoc position in biological intelligence of exploration at CMU & Pitt

by Timothy Verstynen

Carnegie Mellon University and the University of Pittsburgh are seeking applications for a joint, NIH-funded postdoc position on the computational neuroscience of exploration, linking computational models to both human behavioral and rodent optogenetic/electrophysiology data. The successful candidate will work with Professors Jonathan Rubin (Pitt) and Timothy Verstynen (CMU), in collaboration with Professors Eric Yttri (Department of Biological Sciences, CMU) and Cati Vich (Department of Applied Mathematics, Universitat de les Illes Balears, Mallorca, Spain). The project specifically focuses on how dynamics of cortico-basal ganglia-thalamic pathways map to cognitive models of adaptive decision-making. The position is funded for several years, with an initial one-year appointment and an expectation of extension to three years, given that performance is satisfactory. Applicants with a PhD in Mathematics, Applied Mathematics, Computer Science, Computational Neuroscience, Cognitive Neuroscience or a related discipline, and ideally with experience in computing, in dynamical systems, and in computational neuroscience, should apply at: https://cmu.taleo.net/careersection/2/jobdetail.ftl?job=2015566 Carnegie Mellon University and the University of Pittsburgh are both Affirmative Action, Equal Opportunity Employers and value equality of opportunity, human dignity and diversity. Members of all groups under-represented in academia are especially encouraged to apply. Best, Tim Verstynen -- Timothy Verstynen Ph.D. (he/him) Associate Professor Psychology, Carnegie Mellon Neuroscience Institute, & Biomedical Engineering (by courtesy) Co-Director of the CMU-Pitt BRIDGE Center Carnegie Mellon University Pittsburgh, PA 15213 Phone: 412-533-AXN1 (412-533-2961) Lab URL: www.cognitiveaxon.com Center URL: www.bridge-center.org CONFIDENTIALITY NOTICE: This e-mail (including any attachments) contains information that is confidential, proprietary, and/or legally privileged for the sole use of the intended recipient(s). No confidentiality or privilege is waived. Any review or distribution by an unintended recipient is strictly prohibited. If you have received this e-mail in error, please contact the sender immediately and delete all copies, whether electronic or hard copy. Thank you.

Oct. 23, 2020