- Comp-neuro - lists.cnsorg.org

postdoc and PhD positions in Budapest
by Balazs Ujfalussy Oct. 31, 2020

Oct. 31, 2020

The newly established Laboratory of Biological Computation (https://biocomplab.wordpress.com/) is looking for highly motivated postdoctoral fellows and PhD students to investigate the role of hippocampus in model based planning and predictions. The focus of our laboratory is to understand how various biological phenomena (e.g., ion channels, dendritic spikes, synaptic clustering or theta sequences) contribute to the behaviorally relevant computations performed by the hippocampus. To achieve this we develop novel theories connecting hippocampal circuit dynamics to network function, combine biophysical modelling with in vivo-like input patterns and develop new tools for statistical analysis of hippocampal single neuron and populations activity patterns. The positions with a competitive salary are available from January 1st, 2021, initially for 1 year with the possibility of extension up to 5 years. We offer a stimulating environment in the Institute of Experimental Medicine, Budapest and active collaboration with experimental groups in the institute with the potential to get involved in the design of novel 2P imaging and virtual reality experiments in mice and/or in analysing the data. The ideal candidate has a strong background in quantitative disciplines (physics, math, computer science) and is competent in programming (e.g. python, matlab, R, C). It is an advantage to have an experience in biophysical modelling or analysis of in vivo population activity data (imaging or electrophysiology). Please send your CV, publication list, letter of motivation and contact information for at least two references to Balazs Ujfalussy (ujfalussy.balazs(a)koki.hu) The first evaluation round will begin on November 18th, 2020. The positions will remain open until filled. With best regards, Balazs Ujfalussy

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Postdoctoral Fellow, Boston University School of Medicine, Luebke & Killiany labs
by Klaus Wimmer Oct. 30, 2020

Oct. 30, 2020

We are seeking a highly motivated and detail-oriented postdoctoral fellow with a track record in research applying magnetic resonance imaging and image processing. The central goal of the binational (Boston and Barcelona) CRCNS project is to advance our understanding of the computational and neural mechanisms underlying working memory as well as age-related changes to executive function. The successful candidate will lead analyses of structural MRI (T1 TFE scans), resting-state fMRI, and diffusion spectrum imaging (DSI) brain scans with an overall focus on brain morphometry and connectivity. Data generated from the MRI scans will be correlated with behavioral, physiological, and other anatomical data across the adult life span. This work will be part of a highly interdisciplinary project (psychophysics, imaging, anatomy, electrophysiological experiments, innovative data analysis and computational modeling) and includes the possibility for extended research stays at the Center for Mathematical Research in Barcelona, Spain (Wimmer lab <https://sites.google.com/view/wimmerlab>). The appointment as a Boston University School of Medicine postdoctoral fellow (supervised by Jennifer Luebke <http://www.bumc.bu.edu/anatneuro/our-people/faculty/luebke/> and Ronald J. Killiany <http://www.bumc.bu.edu/anatneuro/our-people/faculty/killiany/>) will be for at least 1 year with the possibility for extension based on performance. REQUIRED SKILLS: *Assist in the acquisition of MR data *Set up a pipeline for the analysis of the MRI scans *Manage image sets/data and perform quality assurance on both *Coordinate data sharing between collaborating laboratories in Boston and Barcelona *Preparation of manuscripts and scientific presentations *For questions or informal inquiries contact: Dr. Jennifer Luebke at * *jluebke(a)bu.edu* <jluebke(a)bu.edu> *Application materials must be submitted through **BU's HR website <https://bu.silkroad.com/epostings/index.cfm?fuseaction=app.jobinfo&id=23&jo…>* *.* -- Klaus Wimmer Ramón y Cajal researcher at Centre de Recerca Matemàtica Campus de Bellaterra, Edifici C 08193 Bellaterra (Barcelona) Spain Tel. +34 935 86 85 15 https://sites.google.com/view/wimmerlab

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[jobs] Postdoctoral position in “Cognition for safety and ergonomics for human-robot interaction in unstructured workspaces” at Italian Institute of Technology (IIT)
by Francesco Rea Oct. 29, 2020

Oct. 29, 2020

COgNiTive Architecture for Collaborative Technologies Research Line at Istituto Italiano di Tecnologia in Erzelli, Genoa, is seeking to appoint one postdoctoral position focusing on the assessment of engagement with safety and ergonomic work, the design of proactive measures and counter measures for safety preservation, the optimization of ergonomics, design of software infrastructure for social interaction with the mobile and dexterous co-robot. The first goal of the research is redesigning cognition for safety and ergonomics for human-robot collaboration in manufacturing and construction unstructured workspaces. The second goal is to support the design of new multipurpose robotics for collaboration (co-robots) in manufacturing processes. The selected candidate will work with a multidisciplinary consortium of participants to the recently awarded project VOJEXT, Value Of Joint EXperimentation in digital Technologies for manufacturing and construction (H2020 DT-ICT-03-2020, n. 952197). The candidate will work with different robotic platforms for human-robot interaction in manufacturing and construction sites selected together with the consortium and with different sensorial setups specifically designed to assess ergonomics and safety associated with the workers in unstructured manufacturing and constructions settings. Apply online at https://iit.taleo.net/careersection/ex/jobdetail.ftl?lang=en&job=20000042 The research for this postdoctoral position will involve: * Sensing of human working conditions for social, safe and ergonomic based on human-robot collaboration in unstructured manufacturing and construction settings * Design of control systems for mobile robots for Safety in human-robot collaboration * Development of a system improving human-robot social collaboration in unstructured manufacturing and construction sites * Development of a system improving ergonomics and mitigating health and safety risks in open and unstructured environments

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NEURONUS 2020 IBRO Neuroscience Forum - registration open 3 more days!
by Michał Zaręba Oct. 28, 2020

Oct. 28, 2020

*REGISTRATION for NEURONUS 2020 IBRO Neuroscience Forum (8-11 December 2020, ONLINE) is open only for THREE MORE DAYS! The fee has been reduced to 12€. **More information and registration forms can be found on our website: **http://neuronusforum.pl/* <http://neuronusforum.pl/>*.* The program of the conference consists of numerous sessions on biological, cognitive, computational and medical aspects of neuroscience, creating a dynamic environment for sharing knowledge. The schedule of the meeting is further complemented with lectures by invited guests. This year’s keynote speakers include: - *Karl Friston *(University College London, the UK) - *Pico Caroni *(University of Basel, Switzerland) - *Karin Roelofs *(Radboud University Nijmegen, the Netherlands) - *Alejandro Schinder *(Leloir Institute, Buenos Aires, Argentina) - *Adam Hampshire *(Imperial College London, the UK) - *Dayu Lin *(New York University School of Medicine, the USA) Furthermore, a special panel concerning the Future of Neuroscience will be held. We have confirmed participation of three pioneering researchers: - *Viktor Jirsa *(Aix-Marseille University, France) - *Panayiota Poirazi* (Institute of Molecular Biology and Biotechnology, Heraklion, Greece) - *Dominik Paquet *(Ludwig Maximilian University of Munich, Germany) During the upcoming 11th edition of the conference, we will traditionally continue to put *emphasis on development of early-career researchers*. The main purpose of this event is to provide means for both young and experienced neuroscientists to share the latest discoveries, knowledge and experience in neuroscience, as well as make valuable contacts with scientists representing various fields of neurobiology. We actively promote young scientists through preferentially allocating oral presentations of their experimental results. We strongly encourage you to join this special initiative, and hope to see you soon! On behalf of the Organising Committee, Michał Zaręba

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Launch of World Wide Theoretical Neuroscience Seminar on November, 4, 2020 at 11am EST
by David Hansel Oct. 28, 2020

Oct. 28, 2020

Dear Colleagues, We are happy to announce the launch of the World Wide Theoretical Neuroscience Seminar (WWTNS). WWTNS is a weekly digital seminar on Zoom targeting the theoretical neuroscience community. Its aim is to be a platform of exchange among theoreticians. Speakers have the occasion to talk about theoretical aspects of their work which cannot be discussed in a setting where the majority of the audience consists of experimentalists. The seminars are 45 min long followed by a discussion and are held on Wednesdays at 5 pm in Western Europe, /i.e./, 11 am EST. The talks are recorded with authorization of the speaker and will be available to everybody on our YouTube channel. The first seminar will be on *November, 4, 2020 at 11am EST.* The speaker will be Larry Abbott (Columbia University). The title of his talk is: /Vector Addition in the Navigational Circuits of the Fly/// The abstract of the talk is available on the WWTNS website: http://www.wwtns.online/ *To participate in the seminar you need to fill out a registration form https://www.wwtns.online/register-page after which you will**receive an email telling you how to connect.* We would be grateful if you could forward this email to all those who may be interested. Looking forward to seeing you soon, David Hansel & Carl van Vreeswijk

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PhD position, University of Exeter, UK
by Roman Borisyuk Oct. 28, 2020

Oct. 28, 2020

The University of Exeter is recruiting a PhD student to work on an exciting project to investigate theoretically how neural networks can dynamically transition between multiple behaviours. This BBSRC-funded project is open to students from Mathematics, Physics, Natural Sciences, and Computer Science. The successful candidate will develop new neural network models of rhythmic activity in the tadpole spinal cord. They will use these models to analyse how network behaviour adapts to different sensory inputs. Data for model development will be provided by world-class electrophysiologists, who will also test predictions made by the model. This project will uncover cellular-level and network-level mechanisms that enable dynamic circuit reconfiguration in response to a changing environment. For more information on the project and instructions for applying, please visit http://www.exeter.ac.uk/studying/funding/award/?id=3975. Please contact the project investigators with any question: Joël Tabak j.tabak(a)exeter.ac.uk<mailto:j.tabak@exeter.ac.uk> Roman Borisyuk r.m.borisyuk(a)exeter.ac.uk<mailto:r.m.borisyuk@exeter.ac.uk> ________________________________ [http://www.plymouth.ac.uk/images/email_footer.gif]<http://www.plymouth.ac.uk/worldclass> This email and any files with it are confidential and intended solely for the use of the recipient to whom it is addressed. If you are not the intended recipient then copying, distribution or other use of the information contained is strictly prohibited and you should not rely on it. If you have received this email in error please let the sender know immediately and delete it from your system(s). Internet emails are not necessarily secure. While we take every care, University of Plymouth accepts no responsibility for viruses and it is your responsibility to scan emails and their attachments. University of Plymouth does not accept responsibility for any changes made after it was sent. Nothing in this email or its attachments constitutes an order for goods or services unless accompanied by an official order form.

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Postdoctoral Swartz Fellowship Positions in Theoretical and Computational Neuroscience at Yale
by Murray, John Oct. 28, 2020

Oct. 28, 2020

Postdoctoral Swartz Fellowship Positions in Theoretical and Computational Neuroscience at Yale University The Swartz Center for Theoretical Neurobiology at Yale University invites applications for up to two postdoctoral positions in Theoretical and Computational Neuroscience, with flexible start date in 2021. Competitive candidates include those with a strong quantitative background who wish to gain neuroscience research experience. We especially encourage candidates with an interest in collaborating directly with experimental neuroscientists. The candidates will be expected to perform theoretical/computational studies relevant to one or more laboratories of the Swartz Center at Yale (for a list of affiliated faculty, see: https://medicine.yale.edu/neuroscience/swartz/corelabs.aspx) and will be encouraged to participate in an expanding quantitative biology environment at Yale. Candidates must hold a Ph.D. or equivalent degree by the time of beginning the fellowship. Please send a CV, selected (p)reprints, contact information for two or three references, and a statement of research interests including which laboratories at Yale are of interest. All application materials should be sent electronically to the following e-mail address: john.murray(a)yale.edu<mailto:john.murray@yale.edu>. Applications will be reviewed as they are received, but priority will be given to those received on or before January 15, 2021. For any questions, please contact John Murray. Yale University is an affirmative action/equal opportunity employer. Yale values diversity in its faculty, students, and staff and especially welcomes applications from women and underrepresented minorities. https://neurojobs.sfn.org/job/27534/postdoctoral-swartz-fellowship-position… John D. Murray ----------------------------------------------- Assistant Professor of Psychiatry, Physics, and Neuroscience Yale University murraylab.yale.edu<http://murraylab.yale.edu/> -----------------------------------------------

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SMILES virtual workshop @ICDL 2020
by Xavier Hinaut Oct. 28, 2020

Oct. 28, 2020

The SMILES (Sensorimotor Interaction, Language and Embodiment of Symbols) Workshop will take place virtually at the ICDL 2020 (International Conference on Developmental Learning). * Call for abstracts and papers: - Deadline: 25th of September 2020 - papers abstracts: 2 pages - long papers: 4-6 pages - Submissions: smiles.conf(a)gmail.com <mailto:smiles.conf@gmail.com> - Papers format: same as ICDL conference https://cis.ieee.org/publications/t-cognitive-and-developmental-systems/tcd… <https://cis.ieee.org/publications/t-cognitive-and-developmental-systems/tcd…> - Workshop dates (coming soon): the days before or after the ICDL conference (26-30 October 2020) * Workshop Short Description On the one hand, models of sensorimotor interaction are embodied in the environment and in the interaction with other agents. On the other hand, recent Deep Learning development of Natural Language Processing (NLP) models allow to capture increasing language complexity (e.g. compositional representations, word embedding, long term dependencies). However, those NLP models are disembodied in the sense that they are learned from static datasets of text or speech. How can we bridge the gap from low-level sensorimotor interaction to high-level compositional symbolic communication? The SMILES workshop will address this issue through -an interdisciplinary approach involving researchers from (but not limited to): - Sensori-motor learning, - Emergent communication in multi-agent systems, - Chunking of perceptuo-motor gestures (gestures in a general sense: motor, vocal, ...), - Sensori-motor learning, - Symbol grounding and symbol emergence, - Compositional representations for communication and action sequence, - Hierarchical representations of temporal information, - Language processing and acquisition in brains and machines, - Models of animal communication, - Understanding composition and temporal processing in neural network models, and - Enaction, active perception, perception-action loop. * More info - contact: smiles.conf(a)gmail.com <mailto:smiles.conf@gmail.com> - organizers: Xavier Hinaut, Clement Moulin-Frier, Silvia Pagliarini, Joni Zhong, Loo CHU KIONG, Michael Spranger, Tadahiro Taniguchi - invited speakers (coming soon) - workshop website (comming soon): https://sites.google.com/view/smiles-workshop/ <https://sites.google.com/view/smiles-workshop/> - ICDL conference website: https://cdstc.gitlab.io/icdl-2020/ <https://cdstc.gitlab.io/icdl-2020/> * Workshop Long Description Recently Deep Learning networks have broken many benchmarks in Natural Language Processing (NLP), e.g. [1]. Such breakthroughs are realized by a few mechanisms (e.g. continuous representations like word embedding, attention mechanism, ...). However, no equivalent finding happened towards the understanding of which mechanisms enable the brain to perform similar functions. Deep Learning does not reproduce learning mechanisms nor the dynamics of the brain. The brain needs to parse incoming stimuli and learn from them incrementally, it cannot unfold time like deep learning algorithms such as Back-propagation through time (BPTT). Thus, we still lack the key neuronal mechanisms needed to properly model the (hierarchies of) functions in language perception and production. Other models of language processing reproducing the behavior of brain dynamics (Event-Related-Potentials (ERPs) [2] or functional Magnetic Resonance Imaging (fMRI) [3]) have been developed. However, such model softens lack explanatory power demonstrating the causes of such observed dynamics: i.e. what is computed and why is it computed – for which purpose? We need more biologically plausible learning mechanisms while producing causal explanations of the experimental data modelled. There is converging evidence that language production and comprehension are not separated processes in a modular mind, they are rather interwoven, and this interweaving is what enables people to predict themselves and each other [4].Interweaving of action and perception is important because it allows a learning agent (or a baby) to learn from its own actions: for instance, by learning the perceptual consequences(e.g. the heard sounds) of its own actions (e.g. vocal productions) during babbling [5]. Thus, the agent learns in a self-supervised way instead of relying only on supervised learning, which in contrast, imply non-biological teacher signals cleverly designed by the modeler. Explicit neuronal models explaining which are the mechanisms shaping these perceptuo-motor units through development are missing. The existence of sensorimotor (i.e. mirror) neurons at abstract representation levels (often called action-perception circuits [6]), jointly with the perceptuo-motor shaping of sensorimotor gestures [5], suggest the existence of similar action-perception mechanisms implemented at different levels of hierarchy. How could we go towards such hierarchical architectures based on action-perception mechanisms? Importantly, a language processing model needs a way to acquire the semantics of the (symbolic) perceptuo-motor gestures and of the more abstract representations, otherwise it would consider only morphosyntactic and prosodic featuresof language. These symbolic gestures, i.e. signs, need to be grounded to the mental concept, i.e. signified, they are representing. Several theories and robotic experiments give examples of how symbols could be grounded or how symbols could emerge [7]. However, current neurocomputational models aiming to explain brain processes are not grounded. Robotics have an important role here for the grounding of semantics by experiencing the world through interactions with the physical world and with humans. We need mechanisms that start from raw sensory perception and raw motor commands in order to let emerge plausible representations through development, instead of arbitrary representations. Finally, computational models of emergent communication in agent populations are currently gaining interest in the machine learning community [8], [9]. These contributions show how a communication system can emerge to solve cooperative tasks in sequential environments. However, they are still relatively disconnected from the earlier theoretical and computational literature aiming at understanding how language might have emerged from a prelinguistic substance [10], [11]. We need to conceive communication as the emergent result of a collective behavior optimization process and to ground the resulting computational models into the theoretical literature from language evolution research. The SMILES workshop will aim at discussing each of the questions mentioned above, together with original approaches on how to integrate them. [1] J. Devlin et al., 2018. [2] H. Brouwer and J. C. J. Hoeks, 2013. [3] M. Garagnani et al. 2008. [4] M. J. Pickering and S. Garrod, 2013. [5] J.-L. Schwartz et al., 2012. [6] F. Pulvermüller and L. Fadiga, 2010. [7] T. Taniguchi et al., 2016. [8] S. Sukhbaatar et al.,2016. [9] I. Mordatch and P. Abbeel, 2017. [10] M. Tomasello et al., 2005. [11] P.-Y. Oudeyer and L. Smith, 2015. Xavier Hinaut Inria Researcher (CR) Mnemosyne team, Inria LaBRI, Université de Bordeaux Institut des Maladies Neurodégénératives +33 5 33 51 48 01 www.xavierhinaut.com

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Scientist I position at the Allen Institute - Bio-realistic Modeling of Reconstructed Cortical Tissue
by Anton Arkhipov Oct. 27, 2020

Oct. 27, 2020

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

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New release of the Comp-Neuro Fedora Linux operating system for computational neuroscience is now available for download
by Ankur Sinha Oct. 27, 2020

Oct. 27, 2020

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

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