December 2017 - Comp-neuro - lists.cnsorg.org

Postdoctoral Swartz Fellowship Positions in Theoretical and Computational Neuroscience at Yale University

by Murray, John

The Swartz Center in Theoretical Neurobiology at Yale University invites applications for up to two postdoctoral positions in Theoretical and Computational Neuroscience, with start date mid or late 2018. 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 Yale Swartz Center (https://medicine.yale.edu/neuroscience/swartz/corelabs.aspx) and will be encouraged to participate in an expanding quantitative biology environment. Candidates must hold a Ph.D. or equivalent degree. Please send a Curriculum Vitae, selected reprints, names of those whom we can contact for a reference, and a statement of research plans including the laboratories of interest. All application materials should be sent electronically to the following e-mail address: john.murray at yale.edu <mailto:john.murray at yale.edu>. Applications will be reviewed as they are received, but priority will be given to those received on or before January 20th 2018. For any questions, please contact John Murray <mailto:john.murray at yale.edu>. 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. http://neurojobs.sfn.org/jobs/10584092/ John D. Murray ----------------------------------------------- Assistant Professor Department of Psychiatry Yale University School of Medicine murraylab.yale.edu<http://murraylab.yale.edu/> -----------------------------------------------

Dec. 20, 2017

Assoc Prof and lectureships in Data Science and Predictive Modelling

by Bruce Graham

Dear all, We have 3 new posts at the University of Stirling in Scotland (in addition to 3 posts in Cyber-security, advertised recently and still open for applications). The new posts are an Associate Professor and 2 lecturers in Data Science and Predictive Modelling and are part of an exciting new University of Stirling initiative to strengthen our Computing Science and Mathematics capabilities and collaborations between our Data Science and Biological Modelling research groups and strengthen our related research and teaching. Mathematicians, as well as computer scientists or related disciplines, are particularly encouraged to apply. Computational neuroscience, machine learning, neural networks and other topics of interest to this mailing list fall within the remit of these posts. For complete details and how to apply, please see: https://www.stir.ac.uk/about/jobs/ Closing date is 21st January 2018. For informal enquiries, please email me directly. Best regards, Bruce Graham -- Prof. Bruce Graham (b.graham(a)cs.stir.ac.uk) Professor of Computing Science and Research Director Computing Science and Mathematics Faculty of Natural Sciences University of Stirling Stirling FK9 4LA phone: +44 1786 467 432 fax: +44 1786 464 551 Coauthor of "Principles of Computational Modelling in Neuroscience", CUP 2011. Editorial Board of Journal of Biological Dynamics.

Dec. 19, 2017

Post-doctoral research associate post in Computational Neuroscience, and PhD studentship in Computational Neuroimaging available

by Wong-Lin, Kongfatt

1. A BBSRC funded post-doctoral research associate post in Computational Neuroscience is available at Ulster University, UK. The research project, in collaboration with The University of Oxford, is focused on analyzing and modelling serotonin and related brain systems. For more info, please see: <https://lnkd.in/eDsv3_i> https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTcwMzk4MyZ2dF90… 2. A fully funded Ph.D. studentship in Computational Neuroimaging of Dementia is available at Ulster University. The research project involves close collaboration with academics, clinicians and industrial partners. For more info, please see: <https://lnkd.in/e3scQ_H> https://www.ulster.ac.uk/doctoralcollege/find-a-phd/238180 Please contact me for more information if interested in the post/studentship. Best KongFatt Wong-Lin -------------------------------- E-mail: k.wong-lin(a)ulster.ac.uk https://www.ulster.ac.uk/staff/k-wong-lin This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at postmaster(a)ulster.ac.uk and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of Ulster University. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. Ulster University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The Ulster University was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for Ulster University in Northern Ireland is Cromore Road, Coleraine, Co. Londonderry BT52 1SA

Dec. 19, 2017

Python Exercises and Online textbook: Neuronal Dynamics

by Wulfram Gerstner

We have now finished a series of Python exercises for the book 'Neuronal Dynamics - from single neurons to populations and Models of Cognition' by Gerstner-Kistler-Naud-Paninski (Cambridge Univ. Press) To go directly to the exercises, click here http://neuronaldynamics.epfl.ch/exercises.html An html online version of the book for students (as well as some teaching material for lecturers) is available here: http://neuronaldynamics.epfl.ch <http://neuronaldynamics.epfl.ch/index.html> The pdf of the e-book and printed versions of the book are available via Amazon or Cambridge Univ. Press. The series of exercises has been tested in classes at the EPFL, but we thought that they might be also useful for students at other places, best regards Wulfram Gerstner, Alex Seeholzer, Marco Lehmann EPFL, Switzerland

Dec. 19, 2017

Open position: Coordinator Scientific Computing at Research Center Juelich, Germany

by Martina Reske

Dear Comp-Neuro community The Institute of Neuroscience and Medicine (INM) investigates the structure and function of the human brain on different spatial and temporal scales within the research program “Decoding the Human Brain”. The brain’s high complexity and plasticity over the lifespan of an individual, as well as changes during neuropsychiatric disorders, requires the use of innovative imaging methods and supercomputing technology. Basic neuroscience research heavily relies on modeling and simulation, which are necessary to approach the brain’s immense complexity, manage the huge amount of resulting data, and develop reliable control techniques. Acquired knowledge allows for the translation of basic findings into clinical applications to better understand neurological and psychiatric disorders, to refine diagnostic processes, and to develop therapy strategies – crucial tasks we have to face in ageing societies. The department INM-6, Computational and Systems Neuroscience, develops mathematical models of neuronal dynamics and function. We are active in neuromorphic computing and develop simulation technologies and analysis tools. We are looking to recruit a Coordinator Scientific Computing Your Job: * Design and continuous advancement of a roadmap for scientific computing with regard to hard- and software * Designing a cloud infrastructure and digitized workflows in theoretical neuroscience * Studying international developments in hard- and software in the fields of simulation and data science in neuroscience * Planning, purchasing, set-up and management of UNIX, Linux, Mac OS and Windows systems, communication systems and software * Support of institute’s databases and online tools (webdav, git, wordpress, website); user management * Further development of simulation and analysis codes with regard to system near aspects * Measurement of energy-to-solution and time-to-solution of simulations and analysis codes for scientific studies * Direct support of scientists * Participation in working group leaders’ meeting * Participation in relevant IT committees at Forschungszentrum Juelich * Participation in educating staff in HPC aspects Your Profile: * Completed study of informatics, mathematics or physics * Substantial expertise in C, C++ and Python * Substantial knowledge of UNIX, Windows and Mac OS * Experience with administration of HPC clusters, file, web and print servers as well as with parallel computing (ideally in neuroscience) * Beneficial: Basic knowledge of neuroscience concepts * Ability and willingness to work independently and proactively * Confident appearance and ability to work cooperatively in an interdisciplinary environment * Good interpersonal and communication skills * Structured and systematic working style * Fluent in English (spoken and written) Our Offer: * International, interdisciplinary working environment on an attractive research campus, ideally situated between the cities of Cologne, Düsseldorf, and Aachen * A comprehensive further training Programme * Flexible working hours and various opportunities to reconcile work and family life * Limited for 2 years with possible longer-term prospects * Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD) Forschungszentrum Jülich aims to employ more women in this area and therefore particulary welcomes applications from women. We also welcome applications from disabled persons. We look forward to receiving your application, preferably online<https://www.hrecruiting.de/obf2/bewerbermanagement.php?kunden_nr=t5ChjatkIf…> via our online recruitment system on our career site, quoting the reference number 2017-321. Contact Human Resource Development and Recruiting Kristin Lux Tel.:+49 2461 61 9700 -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Dec. 19, 2017

Operations Research in Neuroscience, Special Issue of Annals of Operations Research

by Ruben A. Tikidji-Hamburyan

Dear colleagues, [apologies for any crossposting] I would like to bring your attention to the special issue on applications of *Operations Research in Neuroscience* recently published in* Annals of Operations Research* Volume *258* Number 1 (Springer). ISSN: 0254-5330 (Print) 1572-9338 (Online) The volume is available online: https://link.springer.com/journal/10479/258/1?wt_mc=alerts.TOCjournals Please find the table of contents below. After a positive response from the journal and the publisher, we are planning to announce another special issue (SI) on the same topic in the same journal early next year. Please let me know if you are interested in contributing to this SI. Best Regards, Ruben ---- Ruben Tikidji-Hamburayn, Ph.D. =================================================================================== Preface *Operations research in neuroscience* Erik Kropat, Ruben A. Tikidji-Hamburyan… Pages 1-4 OR in Neuroscience *A bi-objective network design approach for discovering functional modules linking Golgi apparatus fragmentation and neuronal death* Eduardo Álvarez-Miranda, Hesso Farhan, Martin Luipersbeck… Pages 5-30 OR in Neuroscience *Voxel-MARS: a method for early detection of Alzheimer’s disease by classification of structural brain MRI* Alper Çevik, Gerhard-Wilhelm Weber, B. Murat Eyüboğlu… Pages 31-57 OR in Neuroscience *A semi-supervised inattention detection method using biological signal* Yerim Choi, Jonghun Park, Dongmin Shin Pages 59-78 OriginalPaper *Structure preserving integration and model order reduction of skew-gradient reaction–diffusion systems* Bülent Karasözen, Tuğba Küçükseyhan, Murat Uzunca Pages 79-106 OR in Neuroscience *Totally model-free actor-critic recurrent neural-network reinforcement learning in non-Markovian domains* Eiji Mizutani, Stuart Dreyfus Pages 107-131 OR in Neuroscience *A comparative stationarity analysis of EEG signals* V. Rasoulzadeh, E. C. Erkus, T. A. Yogurt, I. Ulusoy… Pages 133-157 OR in Neuroscience *Anti-periodic solutions for state-dependent impulsive recurrent neural networks with time-varying and continuously distributed delays* Mustafa Şaylı, Enes Yılmaz Pages 159-185

Dec. 19, 2017

Postdoc position in Bristol

by Cian O'Donnell

A postdoctoral position is available to work on statistical analysis and computational modelling of large-scale two-photon imaging data of neural population activity from rodent neocortex. This work is part of a Simons Foundation-funded project that seeks to compare the fidelity and stability of neural coding of sensory stimuli between wild-type mice and Fragile-X Syndrome mouse models. The project is a collaboration between the computational neuroscience group of Cian O’Donnell at University of Bristol (http://seis.bris.ac.uk/~co15268) where you will be based, and the experimental neuroscience group of Carlos Portera-Cailliau at University of California, Los Angeles (https://porteralab.neurology.ucla.edu) You will be part of the growing Bristol Computational Neuroscience Unit (http://www.bris.ac.uk/engineering/research/computational-neuroscience; faculty Rui Costa, Conor Houghton, Nathan Lepora, Naoki Masuda, Rosalyn Moran, and Cian O'Donnell). You should ideally have a PhD in Computational Neuroscience or Machine Learning/Statistics, but we will also accept applications from candidates with PhDs in related disciplines such as Neuroscience, Physics, Mathematics, or Engineering. This post is offered on a full time, open-ended contract with funding for up to 18 months in the first instance. You should be able to start on or before April 2018. Please email Cian O’Donnell (cian.odonnell(a)bristol.ac.uk<mailto:cian.odonnell@bristol.ac.uk>) for informal enquires. More application details here: http://www.jobs.ac.uk/job/BGN179/research-associate-senior-research-associa….

Dec. 18, 2017

Open letter: A commitment to open source in neuroscience

by Andrew Davison

Dear colleagues, We would like to point the members of this list to an initiative which resulted from a workshop on collaborative model development <https://www.janelia.org/you-janelia/conferences/collaborative-development-d…> at Janelia Research Campus. A number of participants agreed to sign an open letter committing to releasing as open source all the software they develop for data analysis and modelling in their publications (whether or not the article is specifically about the software). The letter and current signatories can be found here: http://opensourceforneuroscience.org/ <http://opensourceforneuroscience.org/> A NeuroView article describing this initiative has just been published in Neuron: A Commitment to Open Source in Neuroscience <http://www.cell.com/neuron/fulltext/S0896-6273(17)30981-9>. While many on this list are already sold on the idea of making their own code publicly available, there is another significant statement in the open letter: "If and when asked to serve as peer-reviewers, we will henceforth ask authors about the availability of any code they have developed for data analysis and modelling which is essential to reproducing the results of their paper and require that this be shared publicly upon acceptance." We hope that this public commitment will make it clear to the wider neuroscience community that trying to publish work on the assumption that they will not have to release their code will become more and more difficult, and that the sooner they plan to make it available the better for them and for the wider field. Regards, Padraig Gleeson Andrew P. Davison R. Angus Silver Giorgio A. Ascoli

Dec. 18, 2017

Open position at Institute of Neuroinformatics (Zürich) / Institute of Neuroscience Paris Saclay (Orsay)

by Nicolas Giret

*PhD or Post-Doc for neuroscientist or engineer: neural population activity associated with a complex learned behavior* Dear all, We have an open position for a PhD student or Post-Doc at the interface of engineering and neuroscience. This is a collaborative effort between the Institute of Neuroinformatics (ETH Zurich, University of Zurich) and the Neuroscience Paris Saclay Institute (CNRS, Université Paris Sud, Université Paris Saclay). The goal of our collaboration is to study the principles of vocal learning and communication in songbirds. We combine diverse experimental and theoretical approaches to gain new insights into higher cognitive functions associated with complex vocal behaviors such as song learning. We are interested in decoding neural activity associated with song production and song learning in songbirds. We have recently developed a system for simultaneously recording from many neurons in freely behaving animals. Our miniature lightweight motorized 32-channel recording device incorporates novel carbon fiber electrodes, as described in (Guitchounts, Markowitz, Liberti, & Gardner, 2013). The project is to refine and put this technology to use to study the mysteries of neural population codes and to advance our understanding of how individual neurons contribute to forming a representation of motor plans and of sensory feedback. The engineering part of the work will be done in Zürich, Switzerland (~1/3) and the testing will be done in Orsay, France (~2/3). We are looking either for a PhD student (CHF 47040 starting salary, ~40 200€) or a Post-doc (CHF 80000 starting salary 100%, ~68 500€). Depending on the required training of the post-doc, the employment percentage is reduced to a value between 70 and 90%. Your Profile: You have a MSc degree in neuroscience, electrical engineering, physics, mathematics, biology, or computer science or you have a PhD in neuroscience or engineering. You are strongly interested in neuroscience. You have expertise in signal processing and machine learning. You like to collaborate with biologists and engineers in a nurturing environment. You can work independently and want to be part of a team that fosters flexibility and innovation. The ETH is an equal opportunity employer, we believe in people and their ability to innovate. If you want to apply for this position, feel inspired to send your application material to Prof. Richard Hahnloser (rich(a)ini.ethz.ch <mailto:rich@ini.ethz.ch>) and to Dr Nicolas Giret (nicolas.giret(a)u-psud.fr <mailto:nicolas.giret@u-psud.fr>). It would be great if you could circulate it around in your institute. Best regards, -Nicolas Giret- -- *Chargé de Recherche CNRS* Institut des Neurosciences Paris Saclay, UMR9197 <http://neuro-psi.cnrs.fr/> Université Paris Sud, Univ. Paris Saclay, bât. 446 Rue Claude Bernard 91405 Orsay cedex France 00331.69.15.49.75 Personal website <https://sites.google.com/site/nicolasgiret/>

Dec. 18, 2017

CFP, Special session - Hybrid Life: Approaches to integrate biological, artificial and cognitive systems, ALife 2018

by Manuel Baltieri

[Apologies for cross-posting] ********** Call for Papers ********** Special session - Hybrid Life: Approaches to integrate biological, artificial and cognitive systems https://sites.google.com/view/hybrid-life/ <https://sites.google.com/view/hybrid-life/> 2018 Artificial Life conference (ALife) Tokyo, JAPAN, 23-27 July 2018 - http://2018.alife.org/ <http://2018.alife.org/> --------------------------------------------------------------------------------------------- DESCRIPTION: The main focus of ALife research is the study of natural systems with the goal of understanding what life is. More concretely, ALife defines ways to investigate processes that contribute to the formation and proliferation of living organisms. In this session we focus on three common approaches to tackle this investigation, proposing ways to integrate, extend and possibly improve them. More specifically we refer to: 1) the formalisation of the necessary properties for the definition of life, 2) the implementation of artificial agents, and 3) the study of the relation between life and cognition. For this special session we propose to start from these well-established Alife methodologies, and extend them through: a unified formal language for the description and modelling of living, as well as artificial and cognitive systems, e.g. control theory, Bayesian inference, dynamical systems theory, etc., the exploration of biological creatures enhanced by artificial systems (or artificial systems augmented with organic parts) in order to investigate the boundaries between living and nonliving organisms, and the evaluation of coupled biological-artificial systems that could shed light on the importance of interactions among systems for the study of living and cognitive organisms. This special sessions aims to invite contributions from the fields of psychology, computational neuroscience, HCI, theoretical biology, artificial intelligence, robotics and cognitive science to discuss current research on the formalisation, combination and interaction of artificial/living/cognitive systems from theoretical, modelling and implementational perspectives. Potential topics include, but are not limited to: Formalisation of life and cognition (e.g. dynamical systems theory, stochastic optimal control, Bayesian inference, etc.) Cognitive robotics Autopoiesis Life-mind continuity thesis Systems biology Origins-of-life theories with relationships to artificial and cognitive systems Animal-robot interaction Bio-inspired robotics Bio-integrated robotics Human-machine interaction Augmented cognition Sensory substitution Interactive evolutionary computation Artificial perception Important Dates 19th March 2018 – Paper submission deadline 23rd April 2018 – Paper acceptance notification 21st May 2018 – Camera-ready version 23-27th July 2018 – Artificial Life conference (ALife), Tokyo, Japan Paper Submission Papers and abstracts submitted to this special sessions will be reviewed by a selected group of experts from the a-life community as well as from other areas key to our proposal, specifically chosen for this review process. If you are submitting to a special session you will be given the opportunity to select it during the submission process. Submissions to special sessions follow the same format, instructions and deadlines of regular ALife papers. Organizers Manuel Baltieri, University of Sussex, Brighton, UK. m.baltieri(a)sussex.ac.uk <mailto:m.baltieri@sussex.ac.uk> Keisuke Suzuki, University of Sussex, Brighton, UK. k.suzuki(a)sussex.ac.uk <mailto:filippo.m.bianchi@uit.no> Hiryuki IIzuka, Hokkaido University, Sapporo, Japan hiroyukiiizuka(a)gmail.com <mailto:hiroyukiiizuka@gmail.com> Contacts For questions, enquiries and more information please check our website https://sites.google.com/view/hybrid-life/ <https://sites.google.com/view/hybrid-life/> or get in touch with m.baltieri(a)sussex.ac.uk <mailto:m.baltieri@sussex.ac.uk>. All the best, -- Manuel Baltieri, EASy group Department of Informatics, University of Sussex, UK Twitter: @manuelbaltieri

Dec. 18, 2017