- Comp-neuro - lists.cnsorg.org

GENESIS 2.4 final release now available

by Dave Beeman

The November 2014 GENESIS 2.4 release is the first major revision of the GENESIS 2 neural simulator since the "final" release of GENESIS 2.3 in March 2006. Afterwards, development efforts shifted towards GENESIS 3 (G-3), a 21st century neural simulator without the limitations of GENESIS 2 and other simulators that were developed in the late 1980's and 90's. At this point, G-3 is still in the development stage. Although GENESIS 2.3 was intended to be the last release of the GENESIS 2 series, it has continued to used and to evolve, with modifications needed to efficiently implement synaptic plasticity in large networks and many contributions from users. This has made it necessary for a new November 2014 GENESIS 2.4 release. This new release is now avalable for download from the GENESIS 2 website http://genesis-sim.org/GENESIS/. If any of you will be attending SfN, you can find out more about it at my poster 99.09 (TT88) on Sat, Nov. 15, 2014, 1:00 PM - 5:00 PM The GENESIS 2.4 release includes: * The 'stdp_rules' object, documentation, and Scripts for implementing spike timing dependent plasticity in networks of hsolved cells * New network connection commands allow distance-dependent connection probabilities and/or weights, or the use of periodic boundary conditions for network connectivity. * The chemesis library for modeling second messengers and calcium dynamics * Various user-contributed bug-fixes, utilities, and improvements. * A new autoconf-based build system, so that a simple "./configure" command will create the appropriate Makefile. This has been tested under recent Linux and Mac OSX versions. The older method is also available for platforms not supported by autoconf. * HTML indexing in the 'genesis' directory and subdirectories, for easy browsing of the GENESIS directory system and documentation. * New tutorial Scripts for chemesis, gpython-tools, purkinje, stdp_rules, VAnet2 Dave Beeman ---------------------------------------------------------------------------- Prof. David Beeman, GENESIS Users Group email: genesis(a)genesis-sim.org - dbeeman@.colorado.edu GENESIS WWW site: http://www.genesis-sim.org/GENESIS/ ----------------------------------------------------------------------------

Nov. 12, 2014

[SfN] Computational Neuroscience Social at SfN on Tuesday, November 18

by viola

Dear Colleagues, We write to call your attention to the upcoming computational neuroscience social at the SfN in Washington, DC next week. ** Join us for an evening with elegant models, great spirits, networking theories, and quadrillions of action potentials! Reunite with old friends, make new ones, mingle with top researchers and special guests, and learn about upcoming CompNeuro events. Everyone is welcome! *Special Guests* William Bialek, Kim Blackwell, Nicolas Brunel, Sophie Deneve,Gaute Einevoll, Boris Gutkin, Kenneth Harris, Dietmar Plenz,John Rinzel, Erik De Schutter, Idan Segev, Friedrich T. Sommer, and Tatjana Tchumatchenko We are pleased to confirm the participation of our guest of honor, *Wilfrid Rall.* ** Please feel welcome to *advertise* your summer schools, conferences, tool boxes, journals, associations, or jobs in the field of computational neuroscience in the form of flyers or posters (sugg. max A3, for jobs max A4, poster boards provided), and/or have representative available for informal discussion. *Location: *Renaissance Washington, DC: Renaissance East *Time:* Tuesday, November 18, 6:45-8:45 PM ** Hope to see you in DC! Eilif Muller Viola Priesemann --- Dr. Eilif Muller EPFL - Blue Brain Project Lausanne, Switzerland http://bluebrain.epfl.ch/page-77926-en.html Dr. Viola Priesemann Max Planck Institute for Dynamics and Self-Organization Goettingen, Germany http://www.nld.ds.mpg.de/people/priesemann -- please use my new e-Mail: viola(a)nld.ds.mpg.de MPI for Dynamics and Self-Organization, Göttingen www.nld.ds.mpg.de/people/priesemann

Nov. 11, 2014

Call for Applications: Bernstein Award for Computational Neuroscience 2015

by Kerstin Schwarzwälder

Dear colleagues, I would like to bring to your attention that for the tenth time, the German Federal Ministry of Education and Research (BMBF) has announced an open call for applications for the "Bernstein Award". The "Bernstein Award for Computational Neuroscience" is endowed with up to 1.25 Mio € for a period of five years and allows young scientists of all nationalities to establish an independent research group at a German university or research institution. The BMBF announcement can be found under the following links: German version <http://www.gesundheitsforschung-bmbf.de/de/2476.php> English version <http://www.gesundheitsforschung-bmbf.de/_media/Bernstein_Award_2015_Call_fo…> Posters to announce the Bernstein Award locally can be downloaded from here: German version <http://www.nncn.de/pdfs/poster_ausschreibung_bernsteinpreis2015_de> English version <http://www.nncn.de/pdfs/poster_ausschreibung_bernsteinpreis2015_en> Application deadline is April 15, 2015. Kind 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 fax: +49 761 203 9585 schwarzwaelder(a)bcos.uni-freiburg.de www.nncn.de Twitter: NNCN_Germany <http://twitter.com/NNCN_Germany> YouTube: Bernstein TV <http://www.youtube.com/user/BernsteinNetwork> Facebook: Bernstein Network Computational Neuroscience, Germany <https://www.facebook.com/BernsteinNetwork> LinkedIn: Bernstein Network Computational Neuroscience, Germany <http://www.linkedin.com/company/bernstein-network-computational-neuroscienc…>

Nov. 11, 2014

Release of MOOSE 3.0.0 "Kheer Kadam"

by U.S.Bhalla

We announce the release of MOOSE 3.0.0 "Kheer Kadam" Websites: http://moose.ncbs.res.in, http://sourceforge.net/projects/moose MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models. There are several big changes in 3.0.0:: - Major feature developments for multiscaling, including deterministic reaction-diffusion calculations, a substantial set of classes for Leaky Integrate-and-Fire neuronal networks, and abstract plastic synapses. - Extensive example-based documentation in a new MOOSE Cookbook. - An entirely new and faster messaging system. - An evolution of the Python interface to use object arrays. - Automatic scheduling of all objects upon creation. This release also has a reworked version of the GUI, which is currently in alpha but can be used to run and build kinetic models. About the name: Kheer Kadam is a sweet from Bengal. It has a soft white, dry and sometimes powdery outer layer with a pink or white spongy interior soaked in syrup. Try one! Upi Bhalla will give a talk on MOOSE at the Neuroscience Gateway Workshop at SfN 2014 on Saturday, Nov. 15, 2014. See http://www.nsgportal.org/workshop.html With best regards, The MOOSE team: Subhasis Ray, Harsha Rani, Aditya Gilra, Aviral Goel, Dilawar Singh, Upi Bhalla

Nov. 11, 2014

Doctoral studies at the Princeton Neuroscience Institute

by Yael Niv

The Graduate Program in Neuroscience at Princeton University offers a unique and intensive program of study spanning molecular, cellular, systems and cognitive neuroscience, followed by advanced research in a world-class Princeton laboratory. We seek highly motivated and creative students in our efforts to understand the brain. A listing of faculty affiliated with the program can be found online at www.princeton.edu/neuroscience, and below. Our doctoral program is flexible and individually-tailored, and we encourage students to pursue research with more than one faculty and across departmental boundaries. Applications for entry in the Fall of 2014 are now being accepted, with a deadline of December 1. For details, including contact information, please visit www.princeton.edu/neuroscience. Michael Berry - Neural computation in the retina William Bialek - Interface between physics and biology Matthew Botvinick - Neural foundations of human behavior Lisa Boulanger - Neuronal functions of immune molecules Carlos Brody - Quantitative and behavioral neurophysiology Tim Buschman - Neural dynamics of cognitive control Jonathan Cohen - Neural bases of cognitive control Lynn Enquist - Neurovirology Liz Gavis - Neural development and mRNA localization in Drosophila Alan Gelperin - Learning, memory and olfaction Asif Ghazanfar - Neurobiology of primate social agents Elizabeth Gould - Neurogenesis and hippocampal function Michael Graziano - Sensorimotor integration Charles Gross - Functions of the cerebral cortex in behavior Uri Hasson - Temporal scales of neural processing Philip Holmes - Mathematical modeling John Hopfield - Computational neurobiology/biophysics Barry Jacobs - Brain monoamine neurotransmitters Sabine Kastner - Neural mechanisms for visual perception Carolyn McBride - Molecular and neural basis of behavioral evolution Mala Murthy - Neurophysiology of olfactory and auditory perception in Drosophila Coleen Murphy - Molecular mechanisms of aging Yael Niv - Reinforcement learning and decision making Ken Norman - Neural bases of episodic memory Jonathan Pillow - Neural information processing, machine learning, and statistical modeling of neural data Sebastian Seung - Structure and function of neural circuits Joshua Shaevits - Neural and behavioral dynamics in simple organisms David Tank - Neural circuit dynamics Jordan Taylor - Motor control and learning Alexander Todorov - Cognitive neuroscience of social cognition and behavior Nicholas Turk-Browne - Cognitive neuroscience of attention, perception and memory Samuel Wang - Dynamics and learning in neural circuits Ilana Witten - Neural circuits underlying reward and motivation

Nov. 11, 2014

Faculty positions in applied statistics

by Robert Rosenbaum

Dear colleagues, The ACMS department at Notre Dame is hiring two statistics professors, one tenured and one tenure-track. The department strongly supports interdisciplinary and collaborative research, so researchers who focus on statistical applications in neuroscience are encouraged to apply. Applications should be received by Dec 1. See the full advertisement below. The University of Notre Dame has committed four new faculty positions to the Department of Applied and Computational Mathematics and Statistics (ACMS) to be filled over the next two years. Positions at both the junior and senior level are available. This year we seek to hire a statistician at the tenured level, and a statistician at the tenure-track level, in any areas of research that build on our existing activities. Preference will be given to applicants whose statistical research includes multi-disciplinary collaborations. ACMS includes research groups in applied mathematics, statistics and computational science. The current fourteen faculty members have research interests in Bayesian statistics, statistical bioinformatics and high-dimensional data, finance, statistics in networks and Big Data, multiscale modeling of blood clotting and biofilms, mathematical modeling in cell biology and tumor growth, MEMS, and numerical and computational algorithms and computational neuroscience. ACMS offers a Bachelor of Science, a doctoral degree, a research masters degree and a professional masters degree. ACMS is a member of the College of Science. The successful applicant must have a doctorate in statistics, biostatistics or a closely related field, and a record of success in both research and teaching. The teaching load in ACMS is 3 courses per year, and the position begins in August 2015. Applications received by December 1, 2014 will be given full consideration. Applications, including a cover letter, curriculum vitae and research and teaching statements, should be filed through MathJobs (www.MathJobs.org) Applicants should also arrange for at least three letters of recommendation to be submitted through the MathJobs system. These letters should address the applicant's research accomplishments and supply evidence that the applicant has the ability to communicate articulately and teach effectively. Senior faculty are invited to contact the Department Chair, Steven Buechler, at buechler.1(a)nd.edu, at any time. Notre Dame is an equal opportunity employer, and we particularly welcome applications from women and minority candidates. — Robert Rosenbaum Assistant Professor Department of Applied and Computational Mathematics and Statistics University of Notre Dame

Nov. 11, 2014

Physics of Neural Systems focus topic at the 2015 American Physical Society March Meeting, March 2-6, San Antonio, TX

by Ilya Nemenman

Dear Colleagues: This is the final reminder that the 2015 American Physical Society (APS) March meeting (March 2-6, 2015; San Antonio, TX) will emphasize “Physics of Neural Systems” as one of the focus topics supported by the Division of Biological Physics. We expect multiple sessions resulting from this focus topic, addressing recent advances in understanding of the structure and the dynamics of neural circuits responsible for sensing, memory, and motor output. Arguably, in the last few years, we have found out more about the dynamics of neural circuits than we have in all of the previous decades combined. Thus we solicit submissions of contributed presentations to the March meeting, focusing on a broad range of topics on the intersection of physics and neuroscience, such as quantitative experimental protocols, modeling of neural dynamics, analysis of collective computation in neural circuits, and others. The neural focus at the meeting will be anchored by talks by Tatyana Sharpee (Salk Institute) and Christopher Fang-Yen (University of Pennsylvania), among others. March meeting abstract submission website: http://www.aps.org/meetings/march/scientific/index.cfm <http://www.aps.org/meetings/march/scientific/index.cfm> Abstract submission deadline: November 14, 2014, 5:00pm EST While the actual timing of the neuro sessions at the meeting will not be known until December and will depend on the number of qualified submissions, the sessions will be scheduled not to conflict with other computational neuroscience meetings, such as COSYNE. APS March meeting is the largest physics meeting in the world, attracting about 10,000 physicists. At the meeting, the APS Division of Biological Physics supports one of the largest and scientifically diverse programs on the interface of physics and biology, from molecular and cellular biophysics, to computational neuroscience and population dynamics, featuring typically more than 500 talks every year. We are looking forward to receiving your abstracts. If you have any questions about neuroscience at the March Meeting, please don’t hesitate to contact Ilya Nemenman (ilya.nemenman(a)emory.edu <mailto:ilya.nemenman@emory.edu>). Sincerely, Ilya Nemenman Associate Professor of Physics and Biology Emory University, Atlanta, GA and Vice-Chair, Division of Biological Physics (DBIO) American Physical Society (APS) http://nemenmanlab.org <http://nemenmanlab.org/> Biophysicist? Join APS/DBIO and come to the March Meeting!

Nov. 10, 2014

Can local inhibition lead to long-range competition?

by Dylan Richard Muir

Dear colleagues, We would like to draw your attention to a recent publication, where we examine the spatial range of competition expected for columnar visual cortex, given known features of cortical anatomy. Reprints are freely available from the author’s homepage (see link below). Models of cortex that assume long-range competition are widespread, although it has long been known through anatomical studies that the spatial extent of inhibition is in fact more restricted than that of excitation. We analyzed straightforward models of interacting cortical columns, and performed simulations of larger models, to show how the spatial scales of excitation and inhibition interact to produce competition through disynaptic inhibition. We found that although disynaptic inhibition is widespread, the presence of competition across the cortical surface is predicted well by the anatomy of direct excitatory and inhibitory coupling. In comparison, the effect of multisynaptic network interactions was very small. This implies that for realistic models of cortex, which should include short-range inhibition and longer-range excitation, the spatial extent of competition is likely to be even narrower than the range of inhibitory connections. Muir and Cook, "Anatomical Constraints on Lateral Competition in Columnar Cortical Architectures", Neural Computation 26 8:1624–1666. Reprints: http://dylan-muir.com/resources/docs/neco_a_00613.pdf Journal: http://dx.doi.org/10.1162/NECO_a_00613 Summary: http://dylan-muir.com/projects/lateral_competition_cortex/ Best regards, Dylan Muir. Dylan Muir | Post-doctoral researcher Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel Phone: +41 61 267 17 75 | Email: dylan.muir(a)unibas.ch www.biozentrum.unibas.ch | www.dylan-muir.com

Nov. 10, 2014

Postdoctoral position in computational systems neuroscience (sensory processing & decision-making)

by Ralf Haefner

Postdoctoral position in computational systems neuroscience (sensory processing & decision-making) We are looking for a postdoctoral researcher to join the group of Ralf Haefner in the department for Brain & Cognitive Sciences at the University of Rochester (NY). The focus of our group is on understanding the neural basis of perceptual inference. Based on the assumption that the brain performs probabilistic inference using an internal model of the world, we ask questions such as: What is the nature of the internal model? How is it learnt? How are posterior beliefs represented by spiking responses of populations of neurons and what algorithm does the brain use to compute its beliefs? The position requires strong mathematical and good programming skills. The ideal candidate would also be familiar with machine learning techniques, especially regarding generative models and MCMC-sampling-based probabilistic inference. Possible research projects range from purely theoretical to data-driven. Our collaborations with electrophysiology labs allow for testing of theoretical models using state-of-the-art cortical population recordings in vivo and, if desired, the opportunity to record your own data. More information about past work is available here: http://tinyurl.com/rmhaefner and a preprint of a manuscript representative of future work here: http://arxiv.org/abs/1409.0257 For details on current and possible future projects, and general information, please contact us directly. The successful candidate with join a world-class department with a wide range of research interests ( https://www.bcs.rochester.edu/research/index.html ) and a strong tradition in probabilistic modeling. Start date and duration are flexible. Please send applications including a CV and names of 2-3 references by email. Please contact us as soon as possible if you'd like to meet at the upcoming SfN or NIPS conferences. Ralf Haefner Assistant Professor Brain & Cognitive Sciences University of Rochester (NY) rhaefner(a)bcs.rochester.edu

Nov. 10, 2014

Postdoctoral research position: modelling musical preference decisions

by Marcus Pearce

Dear All (with apologies for cross-posting), A postdoc position is available at Queen Mary, University of London as part of an EPSRC-funded project <http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/M000702/1>on predicting musical choices using computational models of cognitive and neural processing. The goal of the project is to understand the cognitive and neural processes involved in musical preference decisions using computational modelling that incorporates the structure of the music, the listener and the listening context. The project also involves behavioural and EEG data collection and analysis using machine learning. Salary: £31,735 - £35,319 per annum Closing date: 14th November 2014 Start date: January 2014 or soon thereafter Duration of post: 14 Months For further information and to apply see: http://music-cognition.eecs.qmul.ac.uk/postdoc.html Marcus -- Lecturer in Sound and Music Processing Queen Mary, University of London Mile End Road, London E1 4NS, UK Tel: +44 (0)20 7882 6207 Web:http://webprojects.eecs.qmul.ac.uk/marcusp Lab:http://music-cognition.eecs.qmul.ac.uk/

Nov. 10, 2014