- Comp-neuro - lists.cnsorg.org

Call for applications: Brains for Brains Young Researchers' Computational Neuroscience Award 2015

by Kerstin Schwarzwaelder

Dear colleagues, for the sixth time, the Bernstein Association for Computational Neuroscience <http://www.nncn.de/en/bernstein-association> is announcing the "Brains for Brains Young Researchers' Computational Neuroscience Award". The call is open for researchers of any nationality who have contributed to a peer reviewed publication (as coauthor) or peer reviewed conference abstract (as first author) that was submitted before starting their doctoral studies, is written in English and was accepted or published in 2014 or 2015. The award comprises 500 € prize money, plus a travel grant of up to 2.000 € to cover a trip to Germany, including participation in the Bernstein Conference 2015 in Heidelberg (www.bernstein-conference.de) and an individually planned visit to up to two German research institutions in Computational Neuroscience. Deadline for application is May 8, 2015 (5:00 p.m. CET). Detailed information about the application procedure can be found under: www.nncn.de/en/bernstein-association/brains-for-brains-2015 For inquiries please contact info(a)bcos.uni-freiburg.de Best regards, Kerstin Schwarzwälder -- Dr. Kerstin Schwarzwälder Bernstein Coordination Site of the National Bernstein Network Computational Neuroscience Albert Ludwigs University Freiburg Hansastr. 9A 79104 Freiburg Germany phone: +49 761 203 9594 schwarzwaelder(a)bcos.uni-freiburg.de www.nncn.de

April 2, 2015

IJNS Special Issue Call for Papers for "IWSP7: Epilepsy Mechanisms, Models, Prediction & Control"

by Levin Kuhlmann

The International Journal of Neural Systems (IJNS; Impact Factor 6.056) will be publishing a special issue on work presented at the 7th International Workshop on Seizure Prediction "IWSP7: Epilepsy Mechanisms, Models, Prediction & Control" (www.iwsp7.org<http://www.iwsp7.org>) that will be held in Melbourne, Australia, during 3-6 August 2015. The IJNS Special Issue and "IWSP7: Epilepsy Mechanisms, Models, Prediction & Control" will focus on the engineering and science of epilepsy, covering basic mechanisms and imaging, computational modeling for analysis and prediction, and feedback control of epilepsy. Three key themes will be addressed. (1) Seizure prediction from months-to-years long recordings. (2) Model-based data assimilation for time series analysis, neuro-intervention, and feedback control. (3) Multi-modal neuroimaging and computational modelling to assess the spatial origin of seizures and the epileptic network at multiple scales. The following traditional IWSP themes will also be covered: automated seizure detection, prediction and control, seizure physiology mechanisms at multiple scales, high frequency oscillations, epileptic networks, and computational modeling of epilepsy. The call for papers for the special issue can be downloaded from the conference website at the following link: http://www.iwsp7.org/cfp/Epilepsy_Mechanisms_Models_Prediction_and_Control.… As described in the call for papers, invited speakers and researchers submitting the best abstracts to the IWSP7 conference will be invited to submit a manuscript by the IJNS editor-in-chief, Prof. Hojjat Adeli, and the guest editors, Dr Levin Kuhlmann, Prof. Mark J. Cook and Prof. David B. Grayden. We look forward to seeing you at IWSP7! On behalf of the local IWSP7 organizing committee Levin Kuhlmann, PhD David B. Grayden, PhD Mark J. Cook, MD Anthony N. Burkitt, PhD Dean R. Freestone, PhD Tatiana Kameneva, PhD Alan Lai, PhD Elma O'Sullivan-Greene, PhD Andre Peterson, BSc (hons) Email: organizingcommittee(a)iwsp7.org<mailto:organizingcommittee@iwsp7.org>

April 2, 2015

Postdoc positions at IBM Watson Research

by Irina Rish

Computational Biology Department at IBM T.J. Watson is looking for several postdoctoral researchers; see the job descriptions below. Job description 1: https://jobs3.netmedia1.com/cp/faces/job_summary?job_id=RES-0736440 IBM Research is undertaking a project to develop predictive models of neurological and psychiatric disease transitions based on patients’ speech samples and physiological recordings from wearable devices such as accelerometers, heart rate monitors and portable ElectroEncephaloGram (EEG) recorders. The goal of the project is to implement a high sampling frequency system monitoring easily available behavioral and physiological data, and relate these to established psychometric measures of disease, in order to provide neurologist and psychiatrists with high granularity information of the patients’ state, and actionable predictions of imminent transitions. The project will involve a tight collaboration with clinician s. Required Doctorate Degree At least 1 year experience in natural language processing or signal processing At least 1 year experience in Programming (Matlab, Python, C++) English: Intermediate Preferred At least 3 years experience in natural language processing or signal processing At least 2 years experience in Programming (Matlab, Python, C++) At least 2 years experience in psychology and psychiatry At least 2 years experience in cognitive science, big data analytics or wearable computing At least 2 years experience in machine learning English : Fluent Job description 2: https://jobs3.netmedia1.com/cp/faces/job_summary?job_id=RES-0736434 IBM Research is undertaking a project to characterize the progression of neurological diseases using multi-modal imaging techniques, combining state-of-the-art statistical learning and high-performance computing tools with physiological models and mechanistic interpretations. The ultimate goal of this project is to develop an integrative, multi-disciplinary approach to understand underpinning biological mechanisms of disease (e.g. Parkinson’s), as well as provide analytic tools with immediate clinical applicability. The project will involve a tight collaboration with neurobiology researchers and clinicians. IBM is seeking a Postdoctoral Researcher with a degree in neuroimaging, neuroscience, computer science, mathematics, physics, electrical engineering or similar fields. Candidates should have experience in high-throughput brain data modeling, machine learning for big data, computational neuroscience and neurobiology. Candidates with a background in relevant applied mathematics fields such as topological data analysis and optimization will also be considered. Required Doctorate Degree At least 1 year experience in brain imaging, analysis and modeling (magnetic resonance imaging, electroencephalography or magnetoencephalography) Basic knowledge in programming (Matlab, Python, C++) English: Intermediate Preferred At least 3 years experience in brain imaging, analysis and modeling (magnetic resonance imaging, electroencephalography or magnetoencephalography) At least 2 years experience in programming (Matlab, Python, C++) At least 3 years experience in machine learning At least 3 years experience in brain imaging At least 3 years experience in biological psychiatry English : Fluent

April 1, 2015

ANN: HoloViews 1.0 and ImaGen 2.0 released

by James A. Bednar

We are pleased to announce the first public release of HoloViews, a free Python package for scientific and engineering data visualization: http://ioam.github.io/holoviews and version 2.0 of ImaGen, a free Python package for generating two-dimensional patterns useful for vision research and computational modeling: http://ioam.github.io/imagen HoloViews provides composable, sliceable, declarative data structures for building even complex visualizations of any scientific data very easily. With HoloViews, you can see your data as publication-quality figures almost instantly, so that you can focus on the data itself, rather than on laboriously putting together your figures. Even complex multi-subfigure layouts and animations are very easily built using HoloViews. ImaGen provides highly configurable, resolution-independent input patterns, directly visualizable using HoloViews but also available without any plotting package so that they can easily be incorporated directly into your computational modeling or visual stimulus generation code. With ImaGen, any software with a Python interface can immediately support configurable streams of 0D, 1D, or 2D patterns, without any extra coding. HoloViews and ImaGen are very general tools, but they were designed to solve common problems faced by vision scientists and computational modelers. HoloViews makes it very easy to visualize data from vision research, whether it is visual patterns, neural activity patterns, or more abstract measurements or analyses. Essentially, HoloViews provides a set of general, compositional, multidimensional data structures suitable for both discrete and continuous real-world data, and pairs them with separate customizable plotting classes to visualize them without extensive coding. ImaGen 2.0 uses the continuous coordinate systems provided by HoloViews to implement flexible resolution-independent generation of streams of patterns, with parameters controlled by the user and allowing randomness or other arbitrary changes over time. These patterns can be used for visual stimulus generation, testing or training computational models, initializing connectivity in models, or any other application where random or dynamic but precisely controlled streams of patterns are needed. Features: - Freely available under a BSD license - Python 2 and 3 compatible - Minimal external dependencies -- easy to integrate into your workflow - Declarative approach provides powerful compositionality with minimal coding - Include extensive, continuously tested IPython Notebook tutorials - Easily reconfigurable using documented and validated parameters - Animations are supported natively, with no extra work - Supports reproducible research -- simple specification, archived in an IPython Notebook, providing a recipe for regenerating your results - HoloViews is one of three winners of the 2015 UK Open Source Awards To get started, check out ioam.github.io/holoviews and ioam.github.io/imagen! Jean-Luc Stevens Philipp Rudiger Christopher Ball James A. Bednar -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

April 1, 2015

2015 NEURON Summer Course

by Ted Carnevale

This year's NEURON Summer Course has two components that can be taken individually or together. NEURON Fundamentals, which runs from June 20-23, presents what you need to know to use NEURON to model individual neurons and networks of neurons, and introduces parallel simulation. Parallel Simulation with NEURON, which runs from June 24-26, is for users who already know how to write hoc or Python code for NEURON, and need to create models that will run on parallel hardware. Strategies for debugging, and measuring and improving performance, receive special attention. Because of its advanced nature, each day of "Parallel Simulation" includes a block of time in which participants can work on their own projects with expert help close at hand. Registration is limited, and the registration deadline is Friday, May 29, 2015. Discounts are available for applicants who sign up for both courses and/or register by April 20, 2015. For more information see http://www.neuron.yale.edu/neuron/static/courses/nscsd2015/nscsd2015.html --Ted

March 31, 2015

BCF/NWG Course "Analysis and, Models in Neurophysiology" 2015 at the Bernstein Center Freiburg, Germany

by Birgit Ahrens

BCF/NWG Course "Analysis and Models in Neurophysiology" Sunday, October 4 - Friday, October 9, 2015 Bernstein Center Freiburg, Hansastraße 9a, 79104 Freiburg, Germany Aim of the course: The course is intended to provide advanced Diploma/Masters and PhD students, as well as young researchers from the neurosciences with approaches for the analysis of electrophysiological data and the theoretical concepts behind them. The course includes various topics such as: - Neuron Models and Point Processes (Prof. Stefan Rotter) - Local field potentials (Prof. Ulrich Egert) - Neural Coding (Dr. Robert Schmidt) - Neural Decoding (Prof. Carsten Mehring) The course will consist of lectures in the morning and matching exercises using Matlab and Mathematica in the afternoon. The participants should have a basic understanding of scientific programming. This course is designated especially for advanced diploma/master students and PhD students (preferentially in their first year). Application: Please apply by sending one pdf document containing your CV and a meaningful letter of motivation to nwg-course(a)bcf.uni-freiburg.de. The letter of motivation should refer to the following points: - Reasons for wanting to take this course - Background in mathematics - Background in scientific programming - Experience in using Matlab and Mathematica - Background in neuroscience The course is limited to 20 participants. Course fees: NWG members - 50€, others - 125€ Application deadline: June 30, 2015 More information: http://www.bcf.uni-freiburg.de/events/conferences-workshops/20151004-nwgcou… -- *-- Dr. Birgit Ahrens --* Teaching & Training Coordinator Bernstein Center Freiburg University of Freiburg Hansastr. 9a D - 79104 Freiburg Germany Phone: +49 (0) 761 203-9575 Fax: +49 (0) 761 203-9559

March 31, 2015

A "Brain Parts List" for Neurophysiologists - Neuroelectro.org

by Nathan Urban

Dear Colleagues I wanted to alert you to a new publication and an associated resource. We just published a paper entitled: Brain-wide analysis of electrophysiological diversity yields novel categorization of mammalian neuron types in the Journal of Neurophysiology. The paper is available at: http://jn.physiology.org/content/jn/early/2015/03/20/jn.00237.2015.full.pdf Also you might be interested in the associated web site: http://neuroelectro.org The paper describes an approach to collect, compile, validate and analyze data from thousands of published papers describing neurophysiological properties of many types of neurons. In addition to the analyses that we performed, we believe that the data contained in this dataset should be of interest to the broad neurophysiology and modeling community. The data set also would benefit from scientists across the country and world providing feedback, proposing extensions, reporting errors etc. We appreciate any feedback or comments. Best, Nathan Urban - CMU Shreejoy Tripathy - CMU/UBC Shawn Burton - CMU Matt Geramita - U Pittsburgh Rick Gerkin - CMU/ASU -- __________________________________ Nathan Urban, Ph.D. Interim Provost Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences Professor, Department of Biological Sciences Professor, Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave (Biological Sciences) 5000 Forbes Ave (Provost's Office) Pittsburgh PA 15213 ph. 412-268-6684 fax 412-268-2330 http://www.cmu.edu/bio/f <http://www.andrew.cmu.edu/user/nurban/Lab_pages/> aculty/urban.html **For scheduling, please cc Barb Diecks (bdiecks(a)andrew.cmu.edu) on any email

March 31, 2015

Programmer position at the Okinawa Institute of Science and Technology.

by Benjamin Torben-Nielsen

The computational neuroscience unit (De Schutter unit) at the Okinawa Institute of Science and Technology has an opening for a programmer / technician on a neuroinformatics project. Initial duration is one year with an option to extend. Project description: Neuronal morphologies are usually studied in isolation. However, this is in contrast to reality were neurons develop in a dense substrate and actively interact with each other and their environment. Therefore, our group recently developed a computational framework -NeuroMaC- to study how interactions between developing neurons themselves and the environment shape dendrite and axon morphologies. A fully functional prototype of NeuroMaC was implemented in Python. NeuroMaC is designed as a parallel software and implemented using the ZeroMQ messaging library for concurrency. More information about the design and future roadmap of NeuroMac can be found here: http://b-torbennielsen.home.oist.jp/neuromac/neuromac.html#design-requireme… Job description: We seek for a programmer / technician to implement a new version of NeuroMaC using state-of-the-art parallel environments to improve on scalability, execution speed and flexibility. The candidate will be working in the lab headed by Prof. Erik De Schutter and under daily supervision of Dr. Ben Torben-Nielsen. The candidate will help in the final design of the framework and has to be flexible in incorporating additional features as research continues and new requirements are identified. Qualifications: The ideal candidate has extensive experience with parallel programming. We are particularly looking for candidates with experience of (dynamic) load-balancing. Experience with meshing software is a great plus and previous experience with neuroscience is appreciated (but not necessary). * Required: - Extensive experience in developing in Linux environments - Extensive experience in parallel programming (MPI, ZMQ) - Excellent communication skills in English and communication with multi-disciplinary teams - M.Sc. in computer science / physics / computational neuroscience or similar experience * Beneficial: - Familiarity with meshing software (TetGen, gmsh, Cubit, VTK) - Experience in an academic environment - Interest in neuroscience Benefits / Offer: A competitive salary and relocation package are offered. This an ideal position to gain experience in a prominent computational neuroscience lab. Academic contributions by technicians are honoured by authorship on relevant publications. Please contact Prof. Erik De Schutter (erik(a)oist.jp) or Dr. Ben Torben-Nielsen (b.torbennielsen(a)gmail.com) for inquiries. About the workplace: The Okinawa Institute of Science and Technology Graduate University (OIST) will become a model for change in education and research with the best international graduate students, working side by side with world-class faculty in modern well-equipped laboratories. Beautifully situated on the island of Okinawa, OIST relies on a cross-disciplinary approach, with an emphasis on creativity and exchange, to offer unique, individualized graduate training. OIST is a university with no departments, eliminating artificial barriers between people working in different fields, but many nationalities, with students and faculty being attracted from all over the world. Concentrating initially on Neuroscience, Molecular Sciences, Mathematical Sciences, Environmental and Ecological Sciences and Physical Sciences, OIST is bringing some of the best brains in the world to Okinawa to transform the way science and education is done in the global academic world. -- Dr. Ben Torben-Nielsen Computational Neuroscience Unit Okinawa Institute of Science and Technology

March 31, 2015

Poster submission deadline extended to the Fifth International Symposium on Biology of Decision-Making, 11-13 May 2015 @ Paris, France

by Mehdi Khamassi

[Please accept our apologies if you get multiple copies of this message] Dear colleagues, The deadline for poster submission is extended to April 15th for the Fifth International Symposium on Biology of Decision Making (SBDM) which will take place in Paris, France, on May, 11-13th 2015. Poster submission and online registration can be done on the dedicated website: http://sbdm2015.isir.upmc.fr Please circulate widely and encourage your colleagues and team members to attend. ------------------------------------------------------------------------------------------------ FIFTH SYMPOSIUM ON BIOLOGY OF DECISION MAKING (SBDM 2015) May 11-13, 2015, Paris, France Institut du Cerveau et de la Moelle Epinière, Hôpital La Pitié Salpêtrière, Paris, France. & Ecole Normale Supérieure, Paris, France. & Université Pierre et Marie Curie, Paris, France. http://sbdm2015.isir.upmc.fr ------------------------------------------------------------------------------------------------ PRESENTATION: The Fifth Symposium on Biology of Decision Making will take place on May 11-13, 2015 at the Institut du Cerveau et de la Moelle Epinière, Paris, France, with a satellite day at Ecole Normale Supérieure, Paris, France. The objective of this three day symposium is to gather people from different research fields with different approaches (economics, ethology, psychiatry, neural and computational approaches) to decision-making. The symposium will be a single-track, will last for 3 days and will include 6 sessions: (#1) Beyond two: Multi-alternative and multi-attribute choices; (#2) Shaky business: Neural sources of choice variability; (#3) Looking for causality: Choice bias following brain manipulation; (#4) The dark side of choice: Delay, effort and punishment; (#5) Choosing the unknown: The route to exploration; (#6) More brains: Choice in social context. CONFIRMED SPEAKERS: Thomas Boraud (CNRS - Université Bordeaux 2, France) Colin Camerer (California Institute of Technology, USA) Peter Dayan (Gatsby Unit, University College London, UK) Mauricio Delgado (Rutgers University, USA) Sophie Deneve (CNRS - Ecole Normale Supérieure, France) Jan Drugowitsch (Université de Genève, Switzerland) Sylvie Granon (Université d'Orsay - CNRS, France) Hauke Heekeren (Freie Universität Berlin, Germany) Laurence Hunt (University College London, UK) Masud Husain (University of Oxford, UK) Quentin Huys (ETH Zurich - University of Zurich, Switzerland) Miriam Klein-Flügge (University of Oxford, UK) Brian Knutson (Stanford University, USA) Kenway Louie (New York University, USA) John O'Doherty (California Institute of Technology, USA) Mitsuhiro Okada (Keio University, Japan) Kerstin Preuschoff (University of Geneva, Switzerland) Emmanuel Procyk (CNRS - INSERM, France) Christian Ruff (University of Zurich, Switzerland) Aldo Rustichini (University of Minnesota, USA) Liane Schmidt (INSEAD, France) Christopher Summerfield (University of Oxford, UK) Mark Walton (University of Oxford, UK) Melissa Warden (Cornell University, USA) Valentin Wyart (Ecole Normale Supérieure, France) Makiko Yamada (National Institute of Radiological Sciences, Japan) IMPORTANT DATES: April 15, 2015 Extended deadline for Poster Submission April 30, 2015 Deadline for Registration May 11-13, 2015 Symposium Venue ORGANIZING COMMITTEE: Thomas Boraud (CNRS, Bordeaux, France) Sacha Bourgeois-Gironde (La Sorbonne, Paris, France) Kenji Doya (OIST, Okinawa, Japan) Mehdi Khamassi (CNRS - UPMC, Paris, France) Etienne Koechlin (CNRS - ENS, Paris, France) Mathias Pessiglione (ICM - INSERM, Paris, France) CONTACT INFORMATION : Website, registration, poster submission and detailed program: http://sbdm2015.isir.upmc.fr Contact: sbdm2015 [ at ] isir.upmc.fr / sbdm2015-registration(a)isir.upmc.fr -- Mehdi Khamassi, PhD Researcher (CNRS) Institut des Systèmes Intelligents et de Robotique (UMR7222) CNRS - Université Pierre et Marie Curie Pyramide, Tour 55 - Boîte courrier 173 4 place Jussieu, 75252 Paris Cedex 05, France tel: + 33 1 44 27 28 85 fax: +33 1 44 27 51 45 cell: +33 6 50 76 44 92 http://people.isir.upmc.fr/khamassi

March 30, 2015

2 Postdoc Positions in the Frohlich Lab (UNC - Chapel Hill)

by Frohlich, Flavio

Position 1: We are seeking to fill one postdoctoral position in slice electrophysiology in the Frohlich Lab (www.frohlichlab.org<http://www.frohlichlab.org>) at the University of North Carolina at Chapel Hill. We are a rapidly growing lab that aims to understand how cellular and synaptic mechanisms give rise to cortical network dynamics and how these dynamics can be modulated with brain stimulation. We have received grant funding to further grow our slice electrophysiology team in the lab. In particular, we are interested in understanding the role of propagation delays in network synchronization, the study of mesoscale network events by combining optogenetic stimulation and electrophysiology, and elucidating how temporally patterned brain stimulation alters network dynamics. The successful applicant will study such synaptic and intrinsic mechanisms of cortical network dynamics with cutting-edge in vitro slice electrophysiology strategies that combine 120 channel multielectrode array (MEA) electrophysiology, dual patch-clamp, optogenetic stimulation, and real-time closed loop hybrid systems. Requirements: The successful candidate has a PhD in neuroscience or related discipline and a track record of first class science demonstrated by first-author, peer-reviewed scientific articles in the area of in vitro neurophysiology. Documented skills in whole-cell patch clamp recordings are a prerequisite; programming and data analysis skills are essential. Please send your CV and a brief statement of research interest to flavio_frohlich(a)med.unc.edu. Also, please have two letters of recommendation directly submitted to the same email address. Position 2: We are seeking to fill one postdoctoral position in human electrophysiology in the Frohlich Lab (www.frohlichlab.org<http://www.frohlichlab.org>) at the University of North Carolina at Chapel Hill. We are a rapidly growing lab that aims to understand how cortical network dynamics emerge and how these dynamics can be modulated with brain stimulation. We have received grant funding to further grow our human electrophysiology team in the lab. In particular, we are interested in understanding how (feedback) non-invasive brain stimulation alters cortical network dynamics that mediate cognition. The successful applicant will employ tDCS/tACS, EEG, TMS, and cognitive testing for elucidating the functional role of cortical oscillations in cognition and for the development of novel strategies to enhance brain function and treat cognitive deficits in psychiatric disorders such as schizophrenia and autism. Requirements: The successful candidate has a PhD in neuroscience or related discipline and a track record of first class science demonstrated by first-author, peer-reviewed scientific articles in the area of human neurophysiology. Documented skills in EEG and cognitive assays are a prerequisite; programming and data analysis skills are essential. We will provide training in non-invasive brain stimulation methods. Please send your CV and a brief statement of research interest to flavio_frohlich(a)med.unc.edu. Also, please have two letters of recommendation directly submitted to the same email address. -- Flavio Frohlich PhD Assistant Professor Departments of Psychiatry, Cell Biology and Physiology, and Biomedical Engineering Neuroscience Center School of Medicine University of North Carolina at Chapel Hill

March 28, 2015