June 2015 - Comp-neuro - lists.cnsorg.org

NEST, The Neural Simulation Tool, now available on GitHub
by Hans Ekkehard Plesser 19 Jun '15

19 Jun '15

Dear Colleagues! Development of the widely used Neural Simulation Tool NEST for large-scale spiking neuronal network models has now moved to GitHub at https://github.com/nest/nest-simulator The code on GitHub is based on the code base for the coming NEST 2.6.1 bugfix release and is available under GNU Public License version 2 or later. By cloning NEST from our GitHub repository, you will have immediate access to all improvements in the NEST master repository. We would also like to encourage community development contributions to NEST. If you would like to contribute to NEST, you should fork NEST on GitHub and submit your contributions via pull requests. More information: - About the NEST Simulator: http://www.nest-simulator.org - About contributing to NEST: https://nest.github.io/nest-simulator/ - About the NEST Initiative: http://www.nest-initiative.org - User mailing list: http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user - Video about NEST: http://www.youtube.com/watch?v=v0YEiren7D0 About NEST: NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. The development of NEST is coordinated by the NEST Initiative. NEST is ideal for networks of spiking neurons of any size, for example: • Models of information processing e.g. in the visual or auditory cortex of mammals, • Models of network activity dynamics, e.g. laminar cortical networks or balanced random networks, • Models of learning and plasticity. Best regards, Hans Ekkehard Plesser President, The NEST Initiative -- Dr. Hans Ekkehard Plesser, Associate Professor Section Head Dept. of Mathematical Sciences and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.umb.no/~plesser

1 0

Post-doc position at QMUL in 3D vision
by Miles Hansard 18 Jun '15

18 Jun '15

Post-doc position at Queen Mary, University of London: Geometric Evaluation of Stereoscopic Video. A research assistant is sought for this EPSRC project, which will develop a new approach to the evaluation of 3D content, based on computational models of visual perception. Ideas from computer vision will be used to model the geometry of binocular viewing, including the role of eye-movements. A prototype computer vision system will be developed, for the automatic analysis of disparity statistics in stereoscopic video. The output of this system will be targeted at depth-grading and other post-production tasks. The project is in conjunction with a high-profile graphics and visual effects company. There will also be opportunities to work on stereoscopic VR HMD applications. Expertise in scientific programming, including C++ and Matlab, is essential (OpenCV, R, and GPU programming would be useful). Previous work in augmented reality, 3D reconstruction, or psychophysical methods would be an advantage. Please contact Miles Hansard at Queen Mary, University of London (http://www.eecs.qmul.ac.uk/~milesh/) for further information. All nationalities are eligible to apply. For details and procedure see: http://www.jobs.ac.uk/job/ATW277/research-assistant/ -- http://www.eecs.qmul.ac.uk/~milesh/

1 0

Aspect of Neuroscience 2015 - invitation for the conference
by Daniel Borek 18 Jun '15

18 Jun '15

Dear Friends, On behalf of the Board of the Neurobiology Student Scientific Association operating at the Faculty of Biology of the University of Warsaw I would like to invite you to the 5th International Conference " Aspects of Neuroscience" that will be held in Warsaw, Poland, from November 27th to 29th 2015. As in the following years, this time the Conference also consists of poster and report symposia. November symposia will be devoted to: Neurobiology, Cognitive Neuroscience, Clinical Neuroscience and Neuroinformatics. Each of the thematic symposium will be preceded by a lecture delivered by one of the guests, a specialist of a given domain. During the last editions of the conference we had privilege to host such outstanding neuroscientists as Prof. Semir Zeki, Prof. Richard Frackowiak or Prof. Bruce Graham. The conference is intended for students, doctoral students and research workers related to neuroscience. The student lectures will take place simultaneously in two rooms, in basic and extended version. The basic session provides an opportunity to present theoretical and review talks for the students who do not conduct their own research yet. We would like the conference to gather academics with different background and level of expertise, who share the common passion for neuroscience. Language of conference is English. Registration for the conference will be open from July 1st. More information about conference and the whole Project: www.neuronauka.org/eng Find us on facebook: https://www.facebook.com/AspectsOfNeuroscience?fref=ts Yours sincerely, Daniel Borek Neurobiology Student Scientific Association at the University of Warsaw Organizing Committee of the International Conference of Students and Young Scientists "The Aspects of Neuroscience"

1 0

Open position in Juelich, Germany: Koordinator Software Development
by Martina Reske 17 Jun '15

17 Jun '15

Das Forschungszentrum Jülich betreibt interdisziplinäre Spitzenforschung und stellt sich drängenden Fragen der Gegenwart. Es leistet Beiträge zur Lösung großer gesellschaftlicher Herausforderungen in den Bereichen Energie und Umwelt sowie Information und Gehirn. Mit mehr als 5.500 Mitarbeiterinnen und Mitarbeitern gehört es als Mitglied der Helmholtz-Gemeinschaft zu den großen interdisziplinären Forschungszentren Europas. Das Supercomputing Centre, als Standort eines der leistungsfähigsten Rechner, übernimmt eine führende Rolle in der europäischen Exascale Strategie. Das Institut für Neurowissenschaften und Medizin (INM) erforscht im Rahmen des Programms “Decoding the Human Brain” die Organisation des menschlichen Gehirns auf seinen verschiedenen räumlichen und zeitlichen Skalen. Die moderne neurowissenschaftliche Grundlagenforschung erfordert Modellierung und Simulation auf Hochleistungsrechnern, um der Komplexität des Gehirns zu begegnen und Einsicht in seine Arbeitsweise zu gewinnen. Das entstehende Wissen ermöglicht dann die Translation in die klinische Anwendung, um neurologische und mentale Erkrankungen besser zu verstehen, zu diagnostizieren und zu therapieren – Aufgaben, die in einer älter werdenden Gesellschaft von höchster Bedeutung sind. Darüber hinaus werden aber auch Impulse für neue Rechnergenerationen und deren Betrieb gegeben. Das INM-6, Computational and Systems Neuroscience, erstellt mathematische Modelle der Dynamik und Funktion neuronaler Schaltkreise. Dazu gehören die modellgetriebene Analyse der Aktivität und Struktur des Gehirns sowie die Simulation biologisch realistischer Modelle. Die Entwicklung entsprechender Simulationstechnologie und Analysewerkzeuge ist eine wesentliche Komponente der Forschung. Das INM-6 entwickelt zusammen mit seinen Partnern in einem Open Source Ansatz den führenden Code für Simulationen auf der Gehirnskala mit der Auflösung von Nervenzellen (NEST), ist gleichzeitig Teil des Institute of Advanced Simulation (IAS-6, Theoretical Neuroscience) und beherbergt die Coordination Site (BCOS) des nationalen Bernstein Network Computational Neuroscience. Verstärken Sie diesen Bereich als Koordinator Software Entwicklung (w/m) Ihre Aufgaben: * Koordination der Roadmap und der Releases der Simulations-Software NEST * regelmäßige Vorbereitung von und Teilnahme an Koordinierungstreffen und Videokonferenzen zusammen mit oder in Vertretung der Institutsleitung * direkte Betreuung von Wissenschaftlerinnen/Wissenschaftlern und Doktorandinnen/Doktoranden in Bezug auf Software-Entwicklung * Erstellen von Projektberichten und Anträgen * Repräsentation der Simulations-Software auf internationalen Tagungen * Beteiligung an der Weiterentwicklung von Programmen zur Analyse neuronaler Vielkanaldaten * Vertretung des Koordinators Wissenschaftliches Rechnen Ihr Profil: * ein abgeschlossenes Hochschulstudium der Informatik, Mathematik oder Physik * tiefe Kenntnisse/Erfahrungen in C und C++, Python sowie parallelem und verteiltem Rechnen * Fähigkeit und Bereitschaft zu eigenverantwortlichem Handeln, Führungsfähigkeit * Fähigkeit und Bereitschaft selbstständig Projektberichte abzufassen * Erfahrung im Projekt- und Qualitätsmanagement * neurowissenschaftliche Grundkenntnisse, insbesondere neuronaler Dynamik sind von Vorteil * sicheres Auftreten und Kommunikationsvermögen sowie ausgeprägte Fähigkeit zur kooperativen Zusammenarbeit in einer interdisziplinären Arbeitsumgebung * hohe soziale Kompetenz und Fähigkeit zur kooperativen Zusammenarbeit im Team * Bereitschaft zu Reisen * strukturierte und systematische Arbeitsweise * überdurchschnittliches mündliches und schriftliches Kommunikationsvermögen in deutscher und englischer Sprache Unser Angebot: * Integration in ein interdisziplinäres und internationales Institut * Arbeit in einem kreativen Team mit internationaler Perspektive * Zugang zu modernsten Supercomputern und neuromorpher Hardware * die Möglichkeit, Design-Entscheidungen in einem großen Software-Projekt wesentlich mitzubestimmen und zu prägen * enge Zusammenarbeit mit dem Jülich Supercomputing Centre (JSC) und seiner Exascale Strategie insbesondere dem Simulation Laboratory Neuroscience * hohe Sichtbarkeit durch Vertretung der Institutsleitung bei internationalen Projekttreffen * Beteiligung an Publikationen in der Spitzenforschung zur Simulationstechnologie * Arbeit auf Weltniveau an der Grenze zwischen Neurowissenschaft und Technologie an den komplexesten bekannten Systemen * ein grüner wachsender Campus mit den besten weltweit verfügbaren wissenschaftlichen Einrichtungen, nahe den kulturellen Zentren Köln, Düsseldorf und Aachen * eine zunächst auf 2 Jahre befristete Stelle mit der Möglichkeit einer längerfristigen Perspektive * Vergütung und Sozialleistungen nach dem Tarifvertrag des öffentlichen Dienstes (TVöD-Bund) Das Forschungszentrum Jülich möchte mehr Mitarbeiterinnen in diesem Bereich beschäftigen. Wir sind daher an der Bewerbung von Frauen besonders interessiert. Bewerbungen schwerbehinderter Menschen sind uns willkommen. Wir freuen uns auf Ihre Bewerbung, möglichst über unser Online-Bewerbungssystemhttp://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2015-126-DE-INM-6.html?nn=363560 bis zum 07.07.15 unter Angabe der Kennziffer 2015-126. -- 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Postdoctoral Position in Computational Neuroscience at IUPUI
by Yaroslav Molkov 17 Jun '15

17 Jun '15

A postdoctoral/research associate position in computational neuroscience for the duration of up to two years is available in the externally funded project focusing on multiscale computational modeling of motor control mechanisms, involving interactions between basal ganglia, thalamus, cerebellum, cortex, and spinal cord in connection with realistic simulation of pathological changes in motor control during Huntington’s disease. This collaborative project is performed jointly by the groups of Drs. Ilya Rybak (Dept. of Neurobiology and Anatomy, Drexel University, Philadelphia, PA, USA) and Yaroslav Molkov (Dept. of Mathematical Science, Indiana University – Purdue University, Indianapolis, IN, USA). Applicants must have a PhD degree in Neuroscience, Applied Mathematics, Physics, or a related discipline, a strong research record, and excellent C++ programming skills. Previous experience in computational neuronal modeling is a plus. Interested candidates are encouraged to contact Dr. Molkov ( ymolkov(a)iupui.edu) by email. To apply, please send an email along with (1) curriculum vitae; (2) a cover letter describing previous research experience and interests; (3) the names and contact information of three references. ================================= Yaroslav Molkov, Ph.D. Assistant Professor Indiana University - Purdue University at Indianapolis Department of Mathematical Sciences 402 N. Blackford St, LD 270, Indianapolis, IN 46202 Office: LD 224U Phone: (317) 274-6934 Fax: (317) 274-3460 Email: ymolkov(a)iupui.edu

1 0

Postdoctoral position in computational neuroscience
by Maxim Bazhenov 16 Jun '15

16 Jun '15

Applications are invited for post-doctoral research positions in the laboratory of Dr. Maxim Bazhenov at the University of California, Riverside to study role of sleep in memory and learning. This computational neuroscience project involves close collaboration with several experimental laboratories. The ultimate goal of this work is to understand how the interaction among brain areas during different stages of sleep leads to consolidation of memory for recent learning. The successful candidate will be responsible for the design of the anatomically realistic brain network models based on existing experimental data. These models will be used to understand network dynamics that are involved in the processes of memory consolidation, as well as guide data analysis and produce novel experimental predictions. Qualified applicants are expected to have experience in computational/theoretical neuroscience and neural modeling. Programming experience with C/C++ is required. Knowledge of PYTHON or MATLAB is a plus. The University of California offers excellent benefits. Salary is based on research experience. The initial appointment is for 1 year with a possibility of extension. Applicants should send a brief statement of research interests, a CV and the names of three references to Maxim Bazhenov at maksim.bazhenov(a)ucr.edu -- Maxim Bazhenov, Ph.D. Professor, Cell Biology and Neuroscience University of California Riverside, CA 92521 Ph: 951-827-4370 http://biocluster.ucr.edu/~mbazhenov/

1 0

PhD in computational neuroscience, Zurich
by Jean-Pascal Pfister 16 Jun '15

16 Jun '15

Applications are invited for one PhD student position at the Institute of Neuroinformatics (ETHZ, UZH) in Zurich. The position is funded by the Swiss National Science Foundation grant entitled "Inference and Learning with Spiking Neurons". The PhD student will be supervised by Jean-Pascal Pfister in the Theoretical Neuroscience Group. There are several lines of evidence indicating that the human brain performs near Bayesian optimal inference in a wide range of tasks, but it remains unclear how this inference can be implemented in the brain. The aim of the project is to determine how Bayesian inference and learning can be implemented at the level of neurons and synapses. The Institute of Neuroinformatics in Zurich (which is a joint institute belonging to both the Swiss Federal Institute of Technology (ETHZ) and the University of Zurich) offers an ideal environment for studying Computational Neuroscience due to the presence of multiple theoretical and experimental labs. The candidate should hold a Diplom/Master degree in Physics, Mathematics, Machine learning, Computational Neuroscience or a related field. He/she should have a very strong mathematical background, good programming skills and interests in theoretical neuroscience. The position is offered for a period of three years, starting before the 1st of September 2015. Salary scale is provided by the Swiss National Science Foundation (www.snf.ch) The applicant should submit (by email) a CV, a statement of research interests, 2 reference letters, marks obtained for the Diploma/Master, abstract of the Diploma/Master to Jean-Pascal Pfister (jpfister(a)ini.uzh.ch) Deadline for application is 15th of July 2015 or until the position is filled. Jean-Pascal Pfister --------------------------------- Prof. Jean-Pascal Pfister Theoretical Neuroscience Group Institute of Neuroinformatics University of Zurich and ETH Zurich Winterthurerstrasse 190 8057 Zurich, Switzerland www.ini.uzh.ch/~jpfister <http://www.ini.uzh.ch/~jpfister> Tel: +41 44 635 30 79

1 0

PhD/Postdoc positions for neural processor project NPP
by Michael Pfeiffer 15 Jun '15

15 Jun '15

We have a number of available PhD and postdoc positions available now for the Neuromorphic Processor Project (NPP). NPP is a 3 year project that started 1 May 2015. NPP will develop theory, architectures, and FPGA implementations targeting specific applications of deep neural network technology in vision and audition. Deep learning has become the state-of-the-art machine learning approach for sensory processing applications, and this project aims towards real-time, low-power, brain-inspired solutions targeted at full-custom SoC integration. A particular aim of the NPP is to develop efficient data-driven deep neural network architectures that can enable always-on operation on battery-powered mobile devices in conjunction with event-driven sensors. PhD and postdoc positions are available now in theory, hardware architectures, and applications of these networks. For the theory part of the project we are specifically looking for PhD candidates with experience in deep neural networks and/or spiking neural networks, or deep learning applications in vision and audition. The project team includes academic partners in the USA, Canada, and Spain. The project is coordinated by the Institute of Neuroinformatics (INI) at the University of Zurich and ETH Zurich (www.ini.uzh.ch ). INI is a joint institute of the University of Zurich and ETH Zurich and has been cited in IEEE Spectrum and Scientific American as one of the world’s leading organizations in the development of neuromorphic sensing and computing technology. The lead NPP PI is Prof. Tobi Delbruck. Other NPP PIs at INI are Dr. Shih-Chii Liu, Dr. Michael Pfeiffer, and Prof. Giacomo Indiveri. Please see https://docs.google.com/document/d/1MLoZRAYu_--ZH2ORIoqLPLzJs2spXRM0kO2A2QZ… for more details and information on how to apply. Best regards, Michael Pfeiffer, Tobi Delbruck, Shih-Chii Liu, and Giacomo Indiveri -- ========================================= Dr. Michael Pfeiffer Group leader, Program coordinator NSC Institute of Neuroinformatics University of Zurich and ETH Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41 44 635 30 45 Fax +41 44 635 30 53 pfeiffer (at) ini.phys.ethz.ch http://www.ini.uzh.ch/~pfeiffer/ =========================================

1 0

4th Edition of Complex Systems Primer available
by Claudius Gros 15 Jun '15

15 Jun '15

Dear Colleagues, It is a pleasure to announce the availability of the 4th edition of the textbook Complex and Adaptive Dynamical Systems: A Primer (Springer Complexity, Softcover) ISBN: 978-3-319-16264-5 (Print) 978-3-319-16265-2 (Online) by Claudius Gros Complex and adaptive dynamical systems are ubiquitous and the brain constitutes a prominent example. The goal of this book is to provide a general entry point to complex and dynamical systems based on network architectures. ------------------------------------------------------- cover-text: ---------- This primer offers an introduction to the central concepts at the basis of our modern understanding of complex and emergent behavior, together with a detailed coverage of the mathematical methods. All calculations are presented step by step and are straightforward to follow. This new forth edition is fully reorganized and comes with new chapters, figures and exercises. The core of modern complex system sciences are presented in the first chapters, covering network theory, dynamical systems, bifurcation and catastrophe theory, chaos and adaptive processes together with the principle of self-organization in reaction-diffusion systems and social animals. Modern information theoretical principles are treated in further chapters, together with the concept of self-organized criticality, gene regulation networks, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase transitions and the cognitive system approach to the brain. Technical course prerequisites are the standard mathematical tools for an advanced undergraduate course in the natural sciences or engineering. Each chapter comes with exercises and suggestions for further reading, with the solutions to the exercises being provided in the last chapter. ------------------------------------------------------- content: -------- * Chapter 1: Graph Theory and Small-World Networks * Chapter 2: Bifurcations and Chaos in Dynamical Systems * Chapter 3: Dissipation, Noise and Adaptive Systems * Chapter 4: Self Organization and Pattern Formation * Chapter 5: Complexity and Information Theory * Chapter 6: Cellular Automata and Self-Organized Criticality * Chapter 7: Random Boolean Networks * Chapter 8: Darwinian Evolution, Hypercycles and Game Theory * Chapter 9: Synchronization Phenomena * Chapter 10: Elements of Cognitive System Theory * Chapter 11: Solutions to the exercises ------------------------------------------------------- Sincerely, Claudius Gros ***************************************** *** Prof. Dr. Claudius Gros *** *** +49 (0)69 798 47818 *** *** http://itp.uni-frankfurt.de/~gros *** ***************************************** ----------------------------------------------------------- --- Complex and Adaptive Dynamical Systems, A Primer --- --- A graduate-level textbook, Springer (2008/10/13/15) --- -----------------------------------------------------------

1 0

Interdisciplinary PhD Position in Computational Neuroscience of Vision: Active Efficient Coding (AEC)
by Jochen Triesch 14 Jun '15

14 Jun '15

Apologies for cross posting. Please forward to interested students. We have an open PhD student position in my lab (http://fias.uni-frankfurt.de/de/neuro/triesch) at the Frankfurt Institute for Advanced Studies (FIAS) in Frankfurt, Germany to explore the new area of active efficient coding (AEC), a recently formulated generalization of the efficient coding hypothesis to active perception. The basic idea of AEC is that sensory systems learn to use their motor degrees of freedom to contribute to the efficient encoding of sensory signals. Along these lines, we have developed computational models for the self-calibration of active stereo and motion vision [1,2,3]. These models simultaneously learn a sensory representation with sparse coding approaches and controllers for their eye movements through reinforcement learning. Both learning components aim to maximize the overall coding efficiency of the system, which leads to fully self-calibrating sensory-motor loops for active stereo vision (dispartiy tuning and vergence control) and motion vision (motion tuning and pursuit movements). To the best of our knowledge, these models are the first ever to demonstrate how such self-calibration can emerge from a generic efficient coding objective. We have also validated the approach on robots such as the iCub (http://www.icub.org) The work will be performed in a stimulating interdisciplinary environment with ample opportunities for collaboration with neuromorphic engineers, neuroscientists, roboticists, psychologists, and clinicians across the globe. Possible research directions include better understanding how and why such self-calibration can go awry in clinical conditions such as strabism and amblyopia, implementations on neuromorphic hardware and many others. We are seeking an outstanding and highly motivated PhD student for this project. Applicants should have obtained a Masters degree (or equivalent) in Computational Neuroscience or a related field. The ideal candidate will have excellent programming skills (Matlab, Python, C/C++), very good analytic skills, and a broad knowledge of computational neuroscience, machine learning, computer vision, robotics, signal processing and statistics. Furthermore, specific expertise in visual neuroscience, information theory, sparse coding models, and reinforcement learning are desirable. Experience with programming Graphics Processing Units (GPUs) would be a plus. The position can be filled immediately. The Frankfurt Institute for Advanced Studies is a research institution dedicated to fundamental theoretical research in various areas of science. It is embedded into Frankfurt's recently established natural science research campus. Frankfurt itself is the hub of one of the most vibrant metropolitan areas in Europe. It boasts a rich culture and arts community and repeatedly earns highest rankings in worldwide surveys of quality of living. Applications should include a statement of research interests, CV and contact information for at least two references. Send applications to application(a)fias.uni-frankfurt.de. Review of applications will begin immediately. [1] A Unified Model of the Joint Development of Disparity Selectivity and Vergence Control. Zhao Y, Rothkopf CA, Triesch J, Shi B. IEEE Int. Conf. on Development and Learning and Epigenetic Robotics (ICDL), 2012. (Paper of excellence award.) http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=6400876 [2] Robust active binocular vision through intrinsically motivated learning L. Lonini, S. Forestier, C. Teulière, Y. Zhao, B. Shi, J. Triesch, frontiers in Neurorobotics, 2013. http://journal.frontiersin.org/article/10.3389/fnbot.2013.00020/full [3] Self-calibrating smooth pursuit through active efficient coding C. Teulière, S. Forestier, L. Lonini, C. Zhang, Y. Zhao, B. Shi, J. Triesch, Robotics and Autonomous Systems, 2014 http://www.sciencedirect.com/science/article/pii/S0921889014002486 -- Prof. Dr. Jochen Triesch Johanna Quandt Research Professor Frankfurt Institute for Advanced Studies http://fias.uni-frankfurt.de/~triesch/ Tel: +49 (0)69 798-47531 Fax: +49 (0)69 798-47611

1 0