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Fully funded 4-year PhD Position at IIT - Computational approaches to study the neural code
by Stefano Panzeri 04 May '20

04 May '20

Fully funded 4-year PhD Position at IIT - Computational approaches to study the neural code We are seeking candidates for a fully funded 4-year PhD position at the Italian Institute of Technology’s in the lab directed by Stefano Panzeri ( https://www.iit.it/people/stefano-panzeri) We are particularly interested in candidates that wish to work in a project in collaboration with the experimental neurophysiology laboratory of Giuliano Iurilli (https://www.iit.it/people/giuliano-iurilli) We are interested in using mathematical models of neural networks and information theoretic and machine learning analytical tools to understand the principles of neural coding by using as a model the olfactory system. For recent representative publications of Panzeri and Iurilli on relevant topics please see: Chong et al, in press, preprint available at https://www.biorxiv.org/content/10.1101/841916v1 van Vugt B, et al, (2018) Science: DOI: 10.1126/science.aar7186 Runyan C. A., et al (2017) Nature: 548: 92-96 Panzeri, S, et al (2017) Neuron 93: 491-507 Iurilli, G. and Datta, R.S. (2017) Neuron 93 , 1180-1197 Safaai, H. et al (2015) Proc. Natl. Acad. Sci. USA 112(41): 12834–12839 The ideal candidate should have a strong background in numerate sciences, and have a strong propensity for interdisciplinary research. No extensive previous experience in neuroscience is needed. However, a keen interest in understanding the brain is essential. The deadline for the formal application is set to May 27th 2019, but interested candidates are invited me to contact us informally by email ( stefano.panzeri(a)iit.it and Giuliano.urilli(a)iit.it ) as soon as possible, and *no later than May 11th 2020,* by attaching their CV and briefly explaining their interest in this position, to initiate discussion about potential PhD projects of interest. Yours truly, Stefano Panzeri

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PhD position in theoretical and experimental neuroscience
by Nicolas P. Rougier 04 May '20

04 May '20

PhD position in theoretical and experimental neuroscience Application deadline: 30/05/2020 What: PhD position in theoretical and experimental neuroscience Where: Bordeaux, France When: September 2020 (3 years duration) Who: Nicolas Rougier (Inria) & Arthur Leblois (CNRS) A PhD position is available at the Inria Bordeaux Sud-Ouest center and the Institute of Neurodegenerative Disease in Bordeaux, France. Candidate profile ================= The future PhD candidate must have a strong experience at both the theoretical and experimental level. In particular, the following qualities and skills will be highly valued, if not required: * Solid bases in maths and/or physics; * Previous experience in experimental neuroscience; * Programming experience (Python or similar coding language); * Experience in machine learning or data mining is a plus; * Independence and ability to manage a project; * Good English reading/speaking skills. How to apply ============ Please send your application (CV, letter of motivation, and the names and email addresses of one or two persons who can provide recommendation letters) to Dr. Nicolas Rougier (nicolas.rougier(a)inria.fr) and Arthur Leblois (arthur.leblois(a)univ-bordeaux.fr) before the 30th of May 2020. Proposed research ================= Temporally precise movement patterns underlie many motor skills and innate actions, yet the origin of temporal control in motor behaviors remains unclear. While cortical motor regions traditionally have been viewed as encoding features of motor gestures, these models do not address how sequences of motor gestures are produced or appropriately timed. Recently, a number of studies have suggested that, beyond just representing features of motor output, motor regions may have intrinsic oscillatory dynamics or sequential dynamics to act as their own pattern generators. However, in the order of milliseconds, the neural and anatomical correlates of time processing are still largely unknown because the dominant model, which is based on internal clock fails at giving account on experimental data. Understanding the neural dynamics underlying the acquisition and performance of complex sensorimotor tasks has been hindered by the complexity of the underlying brain networks in common animal models used in neuroscience (e.g. rodents or primates). In particular, the complex interactions between cortical areas (primary and secondary motor cortex in rodents, motor, premotor and supplementary motor areas in primates) related to many different sensorimotor associations and motor skills is daunting. Conversely, in birds, the sensorimotor skill of song production and its learning has a dedicated set of interconnected brain nuclei known as the “song system”, making them an outstanding model to study the neural mechanisms of vocal learning and more generally, of sensorimotor learning. Songbirds indeed rely on learned vocalizations to communicate during courtship or aggressive behaviours. Just as speech learning in humans, vocal learning in young birds requires the coordination of vocal muscles to reproduce previously experienced adult vocalizations. Song learning is also limited to a critical period during development and heavily relies on auditory feedback. The proposed research lies at the interface of neurophysiology, cognitive science, applied mathematics, and theoretical physics. The concepts and methods that will be used will draw on single neuron physiology, electrophysiological studies in behaving animals, statistical mechanics, dynamical system theory, and stochastic differential equations. To this end, we will combine a theoretical approach (development of a mathematical model of the timing system) and an experimental one (chronic neural recording in awake birds, behavioural manipulations). Therefore, a collaboration with a team of physiologists at the Institute of Neurodegenerative Diseases, and in particular with Arthur Leblois who has a long-established expertise in the neural mechanisms underlying vocal learning in songbirds. The model will be designed under the supervision of Nicolas Rougier who has extensive experience in computational modelling. Predictions of the model will then be tested experimentally by measuring neuronal activity in the brain areas controlling song timing in songbirds under the supervision of Arthur Leblois. Chronic electrophysiological recordings in singing birds are routinely performed in the lab of Arthur Leblois, and will be implemented in a protocol allowing the induction of plasticity in the duration of song syllables in young adult birds over short periods of time.

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NEST Conference 2020 goes virtual — Call for Contributions
by Hans Ekkehard Plesser 04 May '20

04 May '20

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2020. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will take place as a virtual conference on Monday/Tuesday 29/30 June 2020. We are now inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. Important dates 01 June 2020 — Deadline for submission of contributions 08 June 2020 — Notification of acceptance 10 June 2020 — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) 22 June 2020 — Registration deadline 29 June 2020 — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. _______________________________________________ Neuroinfo mailing list Neuroinfo(a)incf.org<mailto:Neuroinfo@incf.org> https://lists.incf.org/cgi-bin/mailman/listinfo/neuroinfo

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Associate Lecturer (Education-focused) at the University of St Andrews
by Thomas Otto 30 Apr '20

30 Apr '20

Please see the vacancy for a position as Associate Lecturer (Education-focused) at the University of St Andrews. This is a full-time, permanent post, which will primarily focus on delivery of Neuroscience content. Please share with interested colleagues, the advertisement can be found at: https://www.vacancies.st-andrews.ac.uk/Vacancies/W/7074/0/267435/889/associ… -- Dr. Thomas Otto University of St Andrews School of Psychology and Neuroscience St Mary’s Quad, South Street, St Andrews, KY16 9JP, Scotland Phone: +44 (0)1334 462091 http://lclab.wp.st-andrews.ac.uk/

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Fully-funded PhD position at the Vision Institute, Sorbonne University, Paris, France
by angelo.arleo＠inserm.fr 30 Apr '20

30 Apr '20

Fully-funded PhD position at the Vision Institute, Sorbonne University, Paris, France Job description Applications are invited for a 3-year PhD position to develop clinical endpoints of daily-life activity for low vision patients in order to assess visual restoration. The therapeutic benefits of vision restoration are usually evaluated in clinical studies using conventional functional measures such as visual field and contrast sensitivity. However, these tests are not sufficient to characterize the impact of a visual pathology on patients’ quality of life and autonomy. This project will set forth a set of benchmark measures to evaluate a range of daily life functions (locomotion, spatial orientation, posture, balance, reading) in real or virtual conditions. The main goal is to identify behavioral biomarkers of the benefit of vision restoration solutions (namely optogenetic therapy and retinal implants) in visually impaired patients. The PhD candidate will work hand-in-hand with clinicians of the National Hospital Center for Ophthalmology of the Quinze-Vingts and with researchers of the Vision Institute as well as the Streetlab company. The project will be carried out under the supervision of Dr. Colas Authié and Dr. Angelo Arleo. Requirements & eligibility criteria Applicants should have a quantitative background (engineering, computer science, physics, applied mathematics), and a keen interest in behavioral neuroscience. The ideal candidate should have expertise in virtual reality, motor control, and biometric data analysis. Experience in low-vision or knowledge on machine learning and programming languages (Matlab, C or Python) are a plus. Knowledge of French is important (but not mandatory). Proficiency in oral and written English is required. Successful candidates are expected to work in an interdisciplinary environment with engineers, neuroscientists, and clinicians. Applicants must be in the first four years of their research career and they must not have lived in France more than 12 months during the last 3 years. Benefits The position is funded by the Marie Curie ITN project ENTRAIN-VISION and it will start in fall 2020. It corresponds to a full PhD appointment (36 months) with competitive salary and working conditions, monthly mobility allowance, and family allowance (if family obligations). It also provides continuing education, secondments in the private sector, training modules, and transferable skills courses. Working environment The Vision Institute is one of the top international centers for integrated research on vision and eye diseases. It is located at the heart of Paris, on the campus of the National Hospital Center for Ophthalmology of the Quinze-Vingts. The Vision Institute includes multidisciplinary research laboratories, which share state-of-the-art platforms for human and animal experimentation. It also harbors a Clinical Investigation Center, which fosters translational research. The Streetlab provides a panel of unique platforms (reproducing virtual and real immersive environments) and standardized evaluation solutions to measure autonomy, mobility, and quality of life of visually impaired people. How to apply Applicants should apply to the ENTRAIN-VISION consortium (www.entrain-vision.eu <http://www.entrain-vision.eu/>) by May 29th, 2020. For further inquiries, please contact Colas Authié (colas.authie(a)streetlab-vision.com <mailto:colas.authie@streetlab-vision.com>) and/or Angelo Arleo (angelo.arleo(a)inserm.fr <mailto:angelo.arleo@inserm.fr>). *************************************** Angelo ARLEO FONTAINE, PhD Director of Research CNRS Head of the Aging in Vision and Action Lab, Director of the Chair Silversight, Institute of Vision, CNRS - INSERM - Sorbonne University, 17, rue Moreau F-75012 Paris, France Phone: +33 (0)1 53 46 26 52 Mobile: +33 (0)6 46 84 09 56 Email: angelo.arleo(a)inserm.fr Website: www.aging-vision-action.fr

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PhD Positions in Computational Neuroscience at the University of Hertfordshire
by Volker Steuber 30 Apr '20

30 Apr '20

PhD Positions in Computational Neuroscience Biocomputation Research Group Centre for Computer Science and Informatics Research University of Hertfordshire UK Applications are invited for PhD positions in the Biocomputation Research Group at the University of Hertfordshire. Projects involve the development and simulation of models of neurons and neuronal networks to study information processing in the brain and /or the application of machine learning techniques for the analysis of neural data. A description of our research interests and a list of publications can be found on our webpage (http://biocomputation.herts.ac.uk/). Applicants should have excellent computational and numerical skills and a very good first degree in computer science, biology, maths, physics, neuroscience, or a related discipline. Successful candidates are eligible for a research studentship award from the University (GBP 15,009 per annum bursary plus payment of the student fees). Applicants from outside the UK or EU are eligible. Research in Computer Science at the University of Hertfordshire has been recognised as excellent in the latest Research Excellence Framework Assessment, with 50% of the research submitted rated as internationally excellent or world leading. The Centre for Computer Science and Informatics Research provides a very stimulating environment, offering a large number of specialised and interdisciplinary seminars as well as general training and researcher development opportunities. The University is situated in Hatfield, in the green belt just north of London. Please contact Dr Volker Steuber for informal enquiries. Application forms are available under http://www.herts.ac.uk/apply/schools-of-study/computer-science/our-research… and should be returned to [https://www.herts.ac.uk/__data/assets/image/0016/203434/uhsociallogo.png]<http://www.herts.ac.uk/apply/schools-of-study/computer-science/our-research…> The PhD Programme in Computer Science<http://www.herts.ac.uk/apply/schools-of-study/computer-science/our-research…> See a list of exciting research topics www.herts.ac.uk Lynette Spelman and Emma Thorogood Research Student Administrators University of Hertfordshire College Lane Hatfield, Herts AL10 9AB tel: +44 (0)1707 286083 doctoralcollegeadmissions(a)herts.ac.uk The short-listing process will begin on 1 July 2019.

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Postdoctoral Position in Computational Neuroscience, Barcelona
by Alex Roxin 30 Apr '20

30 Apr '20

The Computational Neuroscience Group at the Centre de Recerca Matemàtica in Bellaterra (Barcelona), Spain, is looking for a postdoctoral researcher to model dynamics, plasticity and learning in hippocampal circuits. The goal is to understand how sensory-driven activity in areas CA3 and CA1 during spatial exploration leads to memory formation in rodents. The work involves network modelling as well as the analysis of in-vivo electrophysiological and calcium imaging data provided by experimental collaborators. The ideal candidate has a strong technical background, such as in Computational Neuroscience, Applied Mathematics, Physics or similar. To apply, please send a CV, letter of motivation and the names of two references to Alex Roxin at aroxin(a)crm.cat Applications will be accepted until the position is filled. Pre-application inquiries are also welcome. -- Alex Roxin Computational Neuroscience Group Centre de Recerca Matemàtica Campus de Bellaterra, Edifici C 08193, Bellaterra (Barcelona) Spain https://sites.google.com/site/alexanderroxin/home

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Open positions at the SimLab Neuroscience, Juelich, Germany
by Abigail Morrison 28 Apr '20

28 Apr '20

Dear colleagues, We have two open positions available in the SimLab Neuroscience at the Juelich Supercomputing Centre, Juelich Research Centre, Germany. For the full descriptions and details of how to apply, please see the announcements on our website: Scientific Software Developer with a focus on neuroscience community engagement https://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2020-061-E… Research Scientist – Development of Neuroscience Data Transport Middleware on High-Performance Computing Systems https://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2020-128-E… The deadline for applications is 10 May 2020. All the best, Abigail Morrison -- Prof. Dr. Abigail Morrison IAS-6 / INM-6 / SimLab Neuroscience Jülich Research Center & Computer Science 3 - Software Engineering RWTH Aachen http://www.fz-juelich.de/inm/inm-6 http://www.fz-juelich.de/ias/jsc/slns http://www.se-rwth.de Office: +49 2461 61-9805 Fax # : +49 2461 61-9460 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Workshop on Machine Learning for Pharma and Healthcare Applications (PharML 2020) - Deadline 11 June 2020
by Konstantinos Sechidis 28 Apr '20

28 Apr '20

*** Call For Papers PharML 2020: Machine Learning for Pharma and Healthcare Applications We invite contributions from both industry and academia to share their research and experience in using artificial intelligence and machine learning methods in pharmaceutical research and development. PharML will be held at the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) to take place in Ghent, Belgium, on 14th - 18th of September 2020. Submission Guidelines We invite authors to submit extended abstracts including preliminary results as well as published work. Authors should submit a paper of up to 4 pages (excluding references). Longer papers will be rejected immediately. Priority will be given to unpublished work. Authors should commit to present their work at the workshop in case it is accepted for an oral or poster presentation. All accepted abstracts will be posted on the workshop's website. - All manuscripts will be peer-reviewed, double-blinded - Abstracts should be in PDF format, following the Springer Lecture Notes in Computer Science style https://www.overleaf.com/latex/templates/springer-lecture-notes-in-computer… - Submissions should be done via the workshop EasyChair page https://easychair.org/my/conference?conf=pharml2020# Topics of Interest The following list, although not exhaustive, covers some of the main topics that will be discussed in the workshop. - Learning on Graphs - Representing patients and molecules as graphs - Transfer learning and generative models - Modelling dynamic graphs - Node and link prediction on molecular graphs - Biological pathway mining for cancer biomarker discovery - Machine learning with brain graphs - Causal structure learning from real world data - Deep learning in healthcare and pharmaceutical research - Medical Imaging - Natural Language Processing - Reinforcement learning in computer-assisted procedures - Audio Processing - Time series analysis - Bayesian methods - Modelling uncertainty - Bayesian methods for classification and imputation - Bayesian networks - General machine learning methods for healthcare and pharma - Machine learning for personalized healthcare - Multimodal machine learning (e.g. combining genomics, pathology reports, clinical data to predict survival) - Remote sensing for healthcare applications - Causal inference with observational data - Subgroup discovery and targeted learning - Longitudinal and trajectory data analysis - Medical decision support Workshop Programme The workshop will feature: - Invited keynote speakers from academia (Stephan Günnemann, Technische Universität München) and industry (Fabien Gaire, Roche). - Oral presentations - A poster session The full programme will be posted on the workshop's website in due course. Important dates Submission Deadline: June 11, 2020 Notification: July 09, 2020 Camera ready: TBA Workshop date: TBA (Monday 14th or Friday 18th of September) Committees Organizing Committee - Lee Cooper (Northwestern University, USA) - Naghmeh Ghazaleh (Roche, Switzerland) - Jonas Richiardi (Lausanne University Hospital, Switzerland) - Damian Roqueiro (ETH Zurich, Switzerland) - Diego Saldana (Roche, Switzerland) - Konstantinos Sechidis (Roche, Switzerland) Program Committee - Laura Azzimonti (IDSIA, Switzerland) - Christian Bock (ETH Zurich, Switzerland) - Christoph Freyre (Novartis, Switzerland) - Geoffrey Fucile (University of Basel, Switzerland) - Marius Garmhausen (Roche, Switzerland) - Elisabetta Ghisu (ETH Zurich, Switzerland) - Max Horn (ETH Zurich, Switzerland) - Elina Koletou (Roche, Switzerland) - Valeria De Luca (Novartis, Switzerland) - Matteo Manica (IBM, Switzerland) - Joseph Mellor (University of Edinburgh, UK) - Michael Mitchley (Roche, Switzerland) - Michael Moor (ETH Zurich, Switzerland) - Nikolaos Nikolaou (UCL, UK) - Marilena Oita, (Simply Vision, Switzerland) - Konstantinos Papangelou (University of Manchester, UK) - Laetitia Papaxanthos (Google Brain, France) - Jon Parkinson (University of Manchester, UK) - Maria Giulia Preti (EPFL, Switzerland) - Bastian Rieck (ETH Zurich, Switzerland) - Elizaveta Semenova (AstraZeneca, UK) - Grigorios Tsoumakas (Aristotle University of Thessaloniki, Greece) Venue Colocated with ECML-PKDD, Ghent, Belgium, on September 14-18, 2020. Contact Visit the official website of the workshop for additional details. https://sites.google.com/view/pharml2020 If you have questions, please send us an e-mail to: pharml2020(a)easychair.org

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Announcing the release of the CompNeuro-Fedora OS for Computational Neuroscientists
by Ankur Sinha 28 Apr '20

28 Apr '20

Hello everyone, (Apologies for the cross-posts) The NeuroFedora team is excited to announce the first release of the CompNeuro-Fedora operating system for computational neuroscientists. https://labs.fedoraproject.org/en/comp-neuro/ CompNeuro-Fedora is a Fedora Linux based Free/Open Source operating system that includes a plethora of tools for computational modelling. These tools are built from their sources as per the Fedora packaging guidelines that enforce the current best practices in software development. So, all you have to do is: - download the image, - install it to disk or a virtual machine (or run it "live"), and - get to work! This release of the ISO image is based on the popular GNOME desktop environment. For computational neuroscience, it includes: Auryn, Bionetgen, Calc: calcium-calculator, COPASI, GetDP, GENESIS, MOOSE, NEST simulator, NEURON, PyLEMS, Smoldyn; along with multiple tools used in analysis: the complete Python science stack: NumPy, SciPy, Matplotlib, IPython, SymPy, and Pandas, R, Julia, GNU Octave, GNUPlot, Paraview, and others. Apart from this set of tools, the NeuroFedora team also provides more neuroscience software that can be installed from the Fedora repositories. Additionally, you also have access to the *complete* set of Free/Open Source software packages available for the Fedora Linux distribution. You can read more about the CompNeuro-Fedora release here: https://neuroblog.fedoraproject.org/2020/04/28/fedora-32-computational-neur… NeuroFedora is a Free/Open Source volunteer community based initiative to support the use of Free/Open Source software in Neuroscience. The team consists wholly of volunteers who spend a few hours a week on this project. We would love to hear from you, and for you to join us. We, especially encourage students to join the community to develop their skills while contributing to NeuroFedora. You can learn more about NeuroFedora here: https://neuro.fedoraproject.org You can get in touch with the community using any of our communication channels: https://docs.fedoraproject.org/en-US/neurofedora/communicating/ -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in PhD candidate in computational neuroscience at UH Biocomputation | http://biocomputation.herts.ac.uk/ Research Fellow at the Silver Lab | http://silverlab.org/ Free/Open source community volunteer at the Fedora project | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

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