- Comp-neuro - lists.cnsorg.org

FINAL CALL for Goettingen's 12th annual comp-neuro summer course. DEADLINE: Aug. 6th.
by Maximilian Puelma Touzel July 29, 2014

July 29, 2014

Final call for applicants to apply to the 12th summer course on COMPUTATIONAL NEUROSCIENCE in Göttingen, Germany September 08th - 12th, 2014 Organized by Agostina Palmigiano, Joscha Liedtke and Maximilian Puelma-Touzel Sponsored by -the Bernstein Centre for Computation Neuroscience, Göttingen -the International Max Planck Research School for the Physics of Biological and Complex Systems -the Goettingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences ______________________________ The course is intended to provide graduate students and young researchers from within and outside of neuroscience with working knowledge of theory and analysis methods used in the field and to acquaint them with recent developments therein. The focus of this year's course is modelling and theory of neuronal ensembles. The course includes tutorials and lectures from the following researchers: * Carl Van Vreesijk, Universite Rene Descartes, Paris, France * Claudia Clopath, Imperial College London, London, England * Srdjan Ostojic, École Normale Supérieure, Paris, France * Gasper Tkacik, Institute of Science and Technology, Vienna, Austria * Alfonso Renart, Champalimaud Centre for the Unknown, Lisbon, Portugal The course takes place at the Department of Nonlinear Dynamics of the Max-Planck Institute for Dynamics and Self-Organization, Göttingen. A course fee of 100 Euro includes participation in the tutorials, study materials, and part of the social events. The number of participants is limited to 30. Course language is English. To apply please fill out the application form at: http://www.bccn-goettingen.de/events/cns-course by *August 6, 2014* Best wishes and looking forward to seeing you in Göttingen, Max Puelma Touzel (on behalf of the organizers) Max Planck Institute for Dynamics and Self-Organization Fassberg 17, 37077 Goettingen, Germany +49 551 5176 444 Office +49 (0)176 6 876 2821 Mobile mptouzel(a)nld.ds.mpg.de www.nld.ds.mpg.de

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Postdoc in computational neuroscience
by Joaquín Navajas July 29, 2014

July 29, 2014

Post doc in computational neuroscience (Centre for Systems Neuroscience - University of Leicester, UK) Spike sorting is the classification of single neurons from extra cellular recordings based on their spike shapes. The main focus of your research will be the study and implementation of optimal spike detection and sorting techniques. For this you will study different techniques to improve the spike detection and sorting results and will then implement these advances in a graphic user interphase and in batch codes to run in matlab. Link for more details: http://www.le.ac.uk/jobs/external/SEN00493_Job_Summary.pdf <https://email.le.ac.uk/owa/redir.aspx?C=6xLmoEDA8kadrrcI2z0-IpKjtXikftEISUM…> Informal enquiries are welcome and should be made to Sue Atkinson, Research Centre Manager, sam45(a)le.ac.uk <https://email.le.ac.uk/owa/redir.aspx?C=RXnrNoZO4k-7v7qrCHbb4FuwAk44fdEIFNi…> or 0116 252 3249

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CNS workshop
by Jonathan Rubin July 28, 2014

July 28, 2014

Dear Comp-Neuro members who are attending the CNS*2014 meeting, We are happy to invite you attend the workshop “Dynamics of Disease States” that will take place on Wednesday, July 30th at the CNS*2014 meeting in Quebec. The workshop will be held in room 2104A and the full program is available at: http://wwwhome.math.utwente.nl/~gilssa/cns2014/?page=program best regards, Stephan van Gils and Jon Rubin

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Columbia+Janelia postdoc positions: zebrafish computational neuroscience and machine learning
by Liam Paninski July 28, 2014

July 28, 2014

Colleagues, Will you please circulate this postdoc ad amongst your students or anyone else who might be interested: http://grossmancenter.columbia.edu/zebrafish.html? Thank you. Liam Paninski ------------------------------------------------------------------------------------------ Postdoctoral position in large-scale computational neuroscience A full-time postdoctoral position is available immediately, jointly between Columbia University's Grossman Center for the Statistics of Mind and HHMI's Janelia Research Campus. The aim is to understand whole-brain activity at the cellular level using large-scale computational methods. The position is co-supervised by Liam Paninski, John Cunningham and Larry Abbott (at Columbia) and Jeremy Freeman and Misha Ahrens (at Janelia Research Campus) and is centered around understanding the dynamics of all neurons in the brain of behaving larval zebrafish. We use light-sheet imaging to record simultaneously from most of the ~10^5 neurons during behavior, and use large-scale cluster computing and machine learning, statistics, and modeling to gain insight into how brain-wide network dynamics underlies behavior. The position will be based at Columbia University and HHMI Janelia Research Campus, and we will encourage applicants to spend time at both campuses. Requirements: Qualifications include primarily a strong research portfolio in computational neuroscience, statistical neuroscience, machine learning, or a related field. Backgrounds in analyzing large neural datasets, modeling complex neural systems, and in cutting-edge machine learning will be particularly valuable. These positions are highly quantitative and highly interdisciplinary; applicants should have a PhD in Electrical Engineering, Statistics, Machine Learning, Physics, Applied Mathematics, or Computational Neuroscience. Appointment: The initial appointments will be for one year, and are renewable. Salaries will be set based on experience and skills. Applicants should send an email to zebrafish.computation(a)gmail.com providing: 1. a one-page description of past research experience 2. a one-page description of future research interests and goals 3. a resume of educational and research experience, including publications 4. names of three people who could provide letters of reference All materials should be in pdf or plain text. Applications will be reviewed as they arrive until the positions are filled; interested candidates are encouraged to express their interest early. Due to demand, we may not be able to reply to all applications.

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ONLY FOR STUDENTS - 2 weeks mini computational neuroscience freelance project for students from home
by Robert Schindle July 28, 2014

July 28, 2014

Hello All, We are currently working on a project in the field of computational neuroscience which requires some help with analyzing data and documenting the research within the next 2 weeks. We are looking for someone with good c++ and Python skills. You will be compensated accordingly. If you are interested please contact us immediately so that we can discuss other details and start the work immediately. Thanks a lot, Robert Schindle.

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Postdoctoral Position- Arizona
by Jean-Marc July 26, 2014

July 26, 2014

The Computational and Experimental Neuroscience Laboratory is looking to fill a position for a Postdoctoral Research Fellow. The research project is geared towards understanding the role of awake hippocampal replay in spatial navigation. The techniques used include high density electrophysiology in the behaving rat. The project is multidisciplinary and involves collaboration with a robotics team (University of Florida, Tampa) and a computational neuroscience team (INSERM, Lyon, France). Good communication skills are necessary. This position is appropriate for a computational neuroscientist with some experimental background interested in branching out to experimental neuroscience. Applicants with a subset of the following skill set are strongly encouraged to apply: - Scientific expertise or interests in hippocampus and/or prefrontal-cortex - Electrophysiology (in vivo chronic behaving or in vitro) - Behavioral Neuroscience (rat training/testing) - General laboratory skills (e.g. histology, surgery) - Matlab programming and spike-data analyses Applicant should send a cover letter, CV and the names of at least 2 references to Dr. Jean-Marc Fellous (fellous(a)email.arizona.edu) The search is ongoing and is projected to be completed by October 30th, 2014. Information about the laboratory can be found at: http://amygdala.psychdept.arizona.edu/lab.html The CENL and the University of Arizona are committed to maintaining a diverse and inclusive work environment and women and minorities are encouraged to apply. The University of Arizona is an equal opportunity, affirmative action employer.

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Postdoctoral positions: Memory, motor, & learning dynamics
by Mark Goldman July 25, 2014

July 25, 2014

Two theoretical postdoctoral positions and 1-2 collaborative experiment-theory positions are available in the laboratory of Dr. Mark Goldman at the University of California at Davis.The lab works on a broad range of problems in computational neuroscience ranging from neural coding to dynamics and plasticity of single neurons and networks. Immediate funding is available for a range of projects related to working memory, neural integration, motor learning, and synaptic plasticity as described below.The postdoctoral candidate also would have flexibility to work on a range of issues of his or her choosing.Candidates are expected to have strong training in an analytically rigorous discipline such as theoretical neuroscience, physics, mathematics, computer science, or engineering.The postdoctoral candidate will have ample opportunity to interact within the vibrant computational and systems neuroscience communities at UC Davis and the greater San Francisco Bay Area. Candidates should send a CV, brief statement of previous research and future research interests, and contact information for three references to: Mark Goldman, msgoldman(a)ucdavis.edu. Specific positions with funding include: 1) *Theoretical positions:Dynamics of memory and motor-related neural activity* /Challenging the attractor picture of working memory/.In the traditional attractor picture of working memory, memory storage results from positive feedback processes that lead to the formation of self-sustained attractors.In one project, we are exploring how functionally feedforward, rather than feedback, network architectures can generate flexible codes for storing memories and producing a broad range of input-output transformations.In a second project, we are utilizing methods from engineering control theory to show how balanced cortical networks can utilize negative feedback to stabilize persistent patterns of neural activity. /Multi-scale modeling of neural integration./The oculomotor neural integrator, which transforms eye-velocity encoding motor commands into eye-position encoding commands, is a model system for understanding the mathematical integration of inputs and the maintenance of memory-storing activity.We seek to determine the respective roles of cellular and circuit mechanisms of memory storage in this system.Multi-scale models, from ion channels to behavior, will be generated based upon electrophysiological and optical imaging recordings and optogenetic manipulations performed in our experimental collaborators' laboratories. /Context-dependent memory storage./Recent experiments suggest that the oculomotor neural integrator functions in a context-dependent manner, producing spatially distinct activity patterns depending upon whether eye movements are being made in the context of rapid changes in gaze (saccades) versus smooth tracking of moving objects.We seek to determine the circuit mechanisms underlying this context-dependent activity and to propose general frameworks, applicable to both oculomotor and cortical memory systems, for how multiple context-dependent inputs can be separately stored in a single network. /Role of the granule cell layer in cerebellar motor learning./The eye movement system provides a highly tractable setting for studying motor learning because it is well-characterized experimentally and has fewer degrees of freedom than more complicated movement systems.In collaboration with whole-circuit optical imaging and optogenetic perturbation experiments in the Aksay laboratory at Cornell Medical University and genetic manipulations, electrophysiological recording, and optogenetic perturbations in Jennifer Raymond's laboratory at Stanford University, we are modeling the neural dynamics and coding of cerebellar granule neurons and their relation to Purkinje cell firing and the plasticity of eye movement behaviors. 2) *Experimental positions:* *Development, dynamics, and plasticity of neural networks: *In collaboration with Kim McAllister (kmcallister(a)ucdavis.edu <mailto:kmcallister@ucdavis.edu>), we are seeking to understand the learning rules underlying development and learning in neural networks. We will use cutting-edge technology in patterned substrates, optogenetics, and uncaging in a novel long-term imaging assay for synapse dynamics that allows recording and single synapse or single cell manipulation of neuronal and network activity. These cultured networks will be used to directly test central tenets of Hebbian, spike-timing dependent, and homeostatic learning over development. The applicant will perform these imaging experiments as well as apply theoretical models to better understand and predict our results. *Dynamics of memory and motor-related neural activity:*There are also possibilities for joint experimental-theoretical work with Emre Aksay's laboratory at Weill Medical College of Cornell University (in New York City) on either oculomotor memory storage or cerebellar motor learning, using /in vivo/ two-photon optical recording and stimulation to dissect circuit function and plasticity.Interested candidates should contact Dr. Aksay at ema2004(a)med.cornell.edu <mailto:ema2004@med.cornell.edu>.

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PhD Position in Brain-Inspired Computing (Theory)
by Mihai A. Petrovici July 25, 2014

July 25, 2014

The Kirchhoff-Institut für Physik at the Ruprecht-Karls-Universität Heidelberg (Germany) has an immediate opening for a * PhD Position in Brain-Inspired Computing (Theory)* The position is located in the Electronic Vision(s) Lab of Prof. Karlheinz Meier. The group develops large-scale hardware for brain-inspired computing and investigates novel theoretical paradigms of neural computation. The Heidelberg group works on the development of brain-inspired electronic circuits, so-called neuromorphic systems. These systems implement physical models of neurons and synapses in-silico, with fully configurable parameters and connectivity. Throughout a series of international projects, the hardware systems have evolved from single chips to wafer-scale devices with hundreds of thousands of neurons (Schemmel et al., 2010) and are planned to be further scaled up in the framework of the EU Human Brain project (HBP). The configurability of these systems fosters their use as general-purpose emulation devices for neuroscientific research (Pfeil et al., 2013). Their intrinsic parallelism, low power consumption and high acceleration sets them apart from conventional computing architectures. The heterogeneity of neuromorphic substrates requires novel theoretical approaches (Petrovici et al., 2014). The Heidelberg group is also involved in theoretical research and modeling of spike-based computational principles. In particular, the use of stochasticity for Bayesian inference is a major focus. These models provide useful architectures for machine learning, while at the same time advancing the study of possible computational paradigms in the mammalian neocortex (Petrovici et al., 2013). The successful candidate will join the theory and modeling section of the group in developing new stochastic models that exploit the heterogeneity of the hardware substrate, thereby benefitting from its significant speed advantage over conventional simulators. ------------------------------------------ Candidates are expected to hold a Masters degree or equivalent in Physics, Mathematics, Computer Science or a related discipline. Knowledge in neuroscience is not required but would be an advantage. The candidates should have a deep interest in theoretical and computational neuroscience, as well as excellent mathematical abilities. An important part of their work will consist in acquiring new skills from various fields of neuroscience, as required by the interdisciplinary nature of the research topic. The successful candidates will use complex simulation software and are therefore required to have very good programming skills. ------------------------------------------ Applications should addressed to Prof. Karlheinz Meier (meierk(a)kip.uni-heidelberg.de) and Mihai Petrovici (mpedro(a)kip.uni-heidelberg.de) including the following information in a single pdf-file : - Statement of research - CV - Two names (with email addresses) of suggested referees - Copies of university degrees and additional certificates - URLs of master /diploma) thesis and related publications

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CNS*14 Tutorial on Neuronal Model Parameter Search Techniques
by Cengiz Günay July 24, 2014

July 24, 2014

Dear colleagues, You are invited to attend our shortly upcoming full-day tutorial session at CNS*2014 in Quebec City. *Where:* Organization for Computational Neurosciences (OCNS) Conference, Quebec City Conference Center, Room 2105 *When:* Saturday July 26, 2014 between 9am - 4:30pm *T9: Neuronal Model Parameter Search Techniques* Parameter tuning of model neurons to mimic biologically realistic activity is a non‐trivial task. Multiple models may exhibit similar dynamics that match experimental data – i.e., there is no single “correct” model. To address this issue, the ensemble modeling technique proposes to represent properties of living neurons with a set of neuronal models. Several approaches to ensemble modeling have been proposed over the years, but the two most prevalent parameter tuning methods are systematic “brute‐force” searches [1, 2] and various evolutionary algorithms‐based techniques [3, 4, 5, 6]. Both approaches relay on traversing a very large parameter space (with thousands to millions of model instances), but utilize diametrically different ways to accomplish that. In both cases, however, entire collections of biologically realistic models are generated, whose neural activity characteristics can then be cataloged and studied using a database [1, 2]. The tutorial covers “tips and tricks,” as well as various pitfalls in all stages of model construction, large‐scale simulations on high performance computing clusters [S2], database construction and analysis of neural data, along with a discussion about the strengths and weaknesses of the two parameter search techniques. We will review software implementations for each technique: PANDORA Matlab Toolbox [7][S1] for the brute force method and NeRvolver (i.e., evolver of nerve cells) for evolutionary algorithms. PANDORA was used in recent projects for tuning models of rat globus pallidus neurons [2][M1], lobster pyloric network calcium sensors [8][M2], leech heart interneurons [9][M3,S3] and hippocampal O‐LM interneurons (Skinner Lab, TWRI/UHN and Univ. Toronto). NeRvolver is a prototype of a computational intelligence‐based system for automated construction, tuning, and analysis of neuronal models, which is currently under development in the Computational Intelligence and Bio (logical) informatics Laboratory at Delaware State University [10]. Through the utilization of computational intelligence methods (i.e., Multi‐Objective Evolutionary Algorithms and Fuzzy Logic), the NeRvolver system generates classification rules describing biological phenomena discovered during the process of model creation or tuning. Thus in addition to producing neuronal models, NeRvolver provides–via such rules–insights into the functioning of the biological neurons being modeled. In the tutorial, we will present basic functionalities of the system and demonstrate how to analyze the results returned by the software. We will allocate enough time for Q&A and if participants bring a laptop pre‐loaded with Matlab, they can follow some of our examples. *Lecturers/Organizers:* Cengiz Günay, Anca Doloc-Mihu (Emory University, USA) Vladislav Sekulić (University of Toronto, Canada), Tomasz G. Smolinski (Delaware State University, USA) *References * [1] Astrid A. Prinz, Cyrus P. Billimoria, and Eve Marder. Alternative to hand‐tuning conductance‐based models: Construction and analysis of databases of model neurons. J Neurophysiol, 90:3998–4015, 2003. [2] Cengiz Günay, Jeremy R. Edgerton, and Dieter Jaeger. Channel density distributions explain spiking variability in the globus pallidus: A combined physiology and computer simulation database approach. J. Neurosci., 28(30):7476–91, July 2008. [3] Pablo Achard and Erik De Schutter. Complex parameter landscape for a complex neuron model. PLoS Comput Biol, 2(7):794–804, Jul 2006. [4] Tomasz G. Smolinski and Astrid A. Prinz. Computational intelligence in modeling of biological neurons: A case study of an invertebrate pacemaker neuron. In Proceedings of the International Joint Conference on Neural Networks, pages 2964–2970, Atlanta, GA, 2009. [5] Tomasz G. Smolinski and Astrid A. Prinz. Multi‐objective evolutionary algorithms for model neuron parameter value selection matching biological behavior under different simulation scenarios. BMC Neuroscience, 10(Suppl 1):P260, 2009. [6] Damon G. Lamb and Ronald L. Calabrese. Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One, 8(11):e79267, 2013. [7] Cengiz Günay, Jeremy R. Edgerton, Su Li, Thomas Sangrey, Astrid A. Prinz, and Dieter Jaeger. Database analysis of simulated and recorded electrophysiological datasets with PANDORA’s Toolbox. Neuroinformatics, 7(2):93–111, 2009. [8] Cengiz Günay and Astrid A. Prinz. Model calcium sensors for network homeostasis: Sensor and readout parameter analysis from a database of model neuronal networks. J Neurosci, 30:1686–1698, Feb 2010. NIHMS176368,PMC2851246. [9] Anca Doloc‐Mihu and Ronald L. Calabrese. A database of computational models of a half‐center oscillator for analyzing how neuronal parameters influence network activity. J Biol Phys, 37(3):263–283, Jun 2011. [10] Emlyne Forren, Myles Johnson‐Gray, Parth Patel, and Tomasz G. Smolinski. Nervolver: a computational intelligence‐based system for automated construction, tuning, and analysis of neuronal models. BMC Neuroscience, 13(Suppl 1):P36, 2012. -Cengiz -- Cengiz Gunay Postdoctoral Fellow, Dept. of Biology Visiting Faculty, Dept. of Math & CS Emory University cgunay(a)emory.edu http://www.biology.emory.edu/research/Prinz/Cengiz/

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Announcement: GENESIS 2.4 beta tutorial at CNS
by Hugo Cornelis July 23, 2014

July 23, 2014

This is a public announcement of the GENESIS-2.4 tutorial at the Computational Neuroscience meeting (CNS) in Quebec City and the official public beta release of GENESIS 2.4. This new release includes support for spike-timing dependent plasticity in large networks of multicompartmental cells, bug fixes, comes with new python utilities and tutorial materials. The "Ultimate GENESIS Tutorial Distribution", included in this release, contains updated course materials for the tutorial Constructing biologically realistic neuron and network models with GENESIS. The tutorial brings together material that is available as separate downloads from the GENESIS web site and through the GENESIS Users Group. It includes several simulator-independent tutorials on biologically realistic neural modeling, as well as both tutorial and research simulations that have been implemented with GENESIS. The latest version of this GENESIS tutorial distribution will be available at http://genesis-sim.org/GENESIS/UGTD.html. The GENESIS tutorial at the CNS meeting is introductory and aimed at people who are new to or have only elementary knowledge about the GENESIS-2 simulator, as well as those who have used GENESIS in the past and would like to learn of new developments in cortical network modeling with GENESIS. * introduction and overview ** Why are we doing this? ** resources ** installation and configuration overview * single neuron modeling and visualization * debugging model and script * fast simulations with hsolve * network modeling * spike-timing dependent plasticity During the last hour of the tutorial, I will show in detail how to technically debug models, scripts and source code, at various levels of implementation. The latest news can always be found at http://genesis-sim.org/GENESIS/ -- Hugo -- Hugo Cornelis Ph.D. GENESIS-3 -- lead architect http://www.genesis-sim.org/ Neurospaces Project Architect http://www.neurospaces.org/

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Brian tutorial at CNS meeting in Québec City
by Marcel Stimberg July 23, 2014

July 23, 2014

**Brian tutorial at CNS meeting in Québec City** Everyone interested in simulating spiking neural networks is invited to join us for a tutorial on the "Brian simulator": 9am-4.30pm, Saturday, 26th July 2014 in Québec City The tutorial is part of the OCNS meeting's tutorials (http://www.cnsorg.org/cns-2014-tutorials) and takes place in room 2101 of the Québec City Conference Center. It will demonstrate the use of Brian 2, a major update of the Brian simulator which further improves its flexibility and adds exciting new code generation abilities. We will provide an introduction to Brian in the morning (no prior knowledge of Brian necessary) and discuss more advanced topics (including the new code generation features) in the afternoon. We recommend participants to install the current version of Brian 2 beforehand; installation instructions, the schedule and additional material can be found here: http://briansimulator.org/brian-tutorial-at-cns-2014/ Best regards, Marcel Stimberg

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Faculty Position in Computational Neuroscience at the University of California, Irvine
by Jeff Krichmar July 22, 2014

July 22, 2014

Dear Computational Neuroscientists, The following job position may be of interest to many of you. ************************** University of California, Irvine Faculty Position in Computational Neuroscience The Department of Cognitive Sciences (www.cogsci.uci.edu) at the University of California, Irvine (UCI) invites applications for a faculty position at the Associate or Full Professor level. We are especially interested in candidates who use mathematical, computational, or robotics approaches to study the neural basis of cognition in any of these areas: (1) vision, hearing, and attention; (2) memory and decision-making; (3) learning and development; (4) language. Applicants whose research relates to human behavior are preferred. A strong record of publications and extramural funding is essential. Exceptional candidates at the Assistant Professor level will also be considered. The online application includes: A cover letter, CV, research and teaching statements, 3 recent publications, and contact information for 3-5 referees. Interested candidates can apply for the position at: https://recruit.ap.uci.edu/apply/JPF02452. To ensure full consideration, please complete the application by November 15, 2014. The University of California, Irvine is an Equal Opportunity/Affirmative Action Employer committed to excellence through diversity. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy. ************************** Best regards, Jeff Krichmar Department of Cognitive Sciences 2328 Social & Behavioral Sciences Gateway University of California, Irvine Irvine, CA 92697-5100 jkrichma(a)uci.edu http://www.socsci.uci.edu/~jkrichma

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GENESIS 2.4 beta release and modeling tutorials
by Dave Beeman July 22, 2014

July 22, 2014

There is now a stable public beta release of GENESIS 2.4 available on the web site for the GENESIS neural simulator. Although there have been development releases of GENESIS 3, this is the first new release of GENESIS 2 since the March 2006 release of GENESIS 2.3. This new release was made necessary by the many improvements and user contributions over the past few years, and the incorporation of new objects for efficiently modeling synaptic plasticity in large networks of realistic multicompartmental cells. The final release will be in November 2014. There is also a new July 2014 version of the "Ultimate GENESIS Tutorial Distribution", a complete self-paced GENESIS modeling course, combined with GENESIS binary and source distributions and installation instructions. It provides an easy way to get everything by downloading a single package. This was prepared as course materials for the tutorial "Constructing biologically realistic neuron and network models with GENESIS" to be given on July 26th at CNS 2014. These may be downloaded from the GENESIS 2 home page at http://genesis-sim.org/GENESIS/ Those who wish to follow or contribute to the development of the final release can get the latest versions at the github repository: https://github.com/dbeeman/genesis-2.4beta-files Dave Beeman ------------------------------------------------------------ Prof. David Beeman, GENESIS Users Group Dept. of Electrical, Computer, and Energy Engineering University of Colorado, Boulder, CO 80309 email: genesis(a)genesis-sim.org - dbeeman(a)colorado.edu GENESIS 2 WWW site: http://genesis-sim.org/GENESIS/ ------------------------------------------------------------

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CNS-2014 - Workshop on Cortical Oscillations: Computational Models and Dynamic Mechanisms
by Horacio G. Rotstein July 22, 2014

July 22, 2014

Dear colleague, We would like to bring to your attention the forthcoming Workshop on "Cortical Oscillations: Computational Models and Dynamics Mechanisms" as part of the Computational Neuroscience Meeting, Juy 26 - 31, Quebec City, Canada. The detailed program including the list of speaker and talk titles can be found in the following link: http://web.njit.edu/~horacio/CNS-2014/CNS-2014_WorkshopCorticalOscillations… Sincerely, Mark Kramer and Horacio Rotstein -- Horacio, NY/NJ area. "Az di bobe volt gehat beytsim volt zi geven mayn zeide" (Yiddish expression) Horacio G. Rotstein Associate Professor Department of Mathematical Sciences New Jersey Institute of Technology Newark, NJ, 07102, USA. Graduate Faculty Behavioral Neuroscience Program Rutgers University (NWK) and Federated Department of Biological Sciences Rutgers / NJIT tel: (1-973) 596-5306 e-mail: horacio(a)njit.edu horacior(a)andromeda.rutgers.edu <horacio(a)njit.edu> http://web.njit.edu/~horacio

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Videos online: Workshop on Cortical Spreading Depression (CSD) and Related Neurological Phenomena
by Markus A Dahlem July 22, 2014

July 22, 2014

*18 VIDEOS online available: * *Workshop on Cortical Spreading Depression (CSD) and Related Neurological Phenomena* http://www.fields.utoronto.ca/video-archive/event/294/2014 Organizers: K. C. Brennan (Neurology,U Utah), Markus A. Dahlem (Physics, Humboldt U, Berlin), Huaxiong Huang (Math. & Statistics, York U), Robert M. Miura (Math. Sci. and Biomedical Eng, NJIT) This workshop brought together a group of researchers from the areas of mathematical modeling and clinicians and experimentalists in neuroscience to address some of the fundamental issues related to neurovascular coupling and cortical spreading depression (CSD) and related neurological phenomenon. 1. Bernice Grafstein: Spreading depression as a holistic process: A historical perspective 2. Cenk Ayata: Spreading depression and the biological heterogeneity of cerebral blood flow response: clues for modeling 3. Huaxiong Huang: Modeling cortical spreading depression and related phenomena 4. Steven Schiff: Unification in the Observation and Control of Spikes, Seizures, and Spreading Depression 5. Jessica Seidel: Cerebral Venous Potassium Efflux During Spreading Depression 6. David Terman: Blocking spreading depolarizations in a neuron/astrocyte network model 7. Jed Hartings: Spreading depolarizations in acute brain injury: mathematical dynamic instability of cerebral cortex? 8. Béla Joós: The Nav coupled left shift model of axon damage: how minor damage can cause major grief 9. Ghanim Ullah: Towards a model-based control of neuronal systems 10. Jorge Manuel Mendez: In vivo cellular dynamics in cortical spreading depression 11. Ernest Barreto: Ion Concentration Dynamics and its Effects on Neuronal Excitability and Bursting 12. Bas-Jan Zandt: Dynamics of single neurons and populations during spreading depolarization 13. Niklas Hübel: Dynamics from seconds to hours in HodgkinHuxley model with time- dependent ion concentrations and buffer reservoirs 14. Markus A. Dahlem: Ghost behavior: Transient localized patterns of CSD in the gyrified human cortex 15. K.C. Brennan: Minimum conditions for the induction of CSD 16. Edward Dudek: Perinatal hypoxic-ischemic encephalopathy: electrographic seizures vs background supression 17. David Andrew: Spreading depolarization strength during ischemia determines higher brain susceptibility and lower brain resistance to acute injury 18. Yoichiro Mori: Modeling ionic electrodiffusion and osmosis in spreading depression If you are interested in updates and upcoming events on this topic, please sent an email to dahlem(a)physik.hu-berlin.de -- Dr. Markus A. Dahlem Humboldt-Universität zu Berlin AG NLD Cardiovascular Physics Robert-Koch-Platz 4 10115 Berlin Germany phone: +49 (0)30 2093 99185 email: dahlem(a)physik.hu-berlin.de skype: markus.dahlem web: https://sites.google.com/site/markusadahlem

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OCNS Workshop on Modeling of Neuron-Glia Interactions, Quebec City, July 30-31.
by Maurizio De Pittà July 22, 2014

July 22, 2014

Dear Sirs, I would kindly ask you to please forward the following message to the comp-neuro mailing list, and further encouraging you to share it with your colleagues. Thanks in advance for your consideration of the matter. Sincerely, Maurizio De Pitta' -------------------------------------------------------------- Dear colleague, we would like to bring at your attention the forthcoming OCNS workshop on "Computational Methods and Modeling of Astrocyte Physiology and Neuron-Glia Interactions". The workshop will take place in Quebec City (Canada) on July 30th-31st, following the main OCNS meeting. The workshop brings together a representative pool of theoreticians involved in modeling of several aspects of astrocyte physiology and neuron-glia interactions, aiming at providing a rare and original occasion to familiarize with the current state of research on the challenging topic of the functional role of neuron-glia interactions. Topics covered by this workshop include: 1. -- Calcium signaling in astrocytes (from subcellular/compartmentalized to network levels); 2. -- Neuron-glia interactions, regulation of synaptic transmission, plasticity and neuronal responses by astrocytes; 3. -- Astrocyte role in homeostasis and neurotrasmitter clearance; 4. -- Information processing by astrocytes. For the detailed program and the list of speakers, you are kindly invited to visit the workshop homepage: https://team.inria.fr/beagle/ocns-2014-workshop/ We encourage you to share this mail with your colleagues and whoever could be interested to attend our workshop. Thanks for your attention. Kind regards, Maurizio De Pitta' Hugues Berry -------------------------------------------------------------------------------- Maurizio De Pitta' - https://sites.google.com/site/mauriziodepitta Hugues Berry - http://www.inrialpes.fr/Berry -------------------------------------------------------------------------------- Project-Team BEAGLE INRIA Rhone-Alpes Université de Lyon LIRIS UMR5205 Antenne INRIA de La Doua Batiment CEI-1 66 Blvd Niels Bohr CS 52132 69603 Villeurbanne cedex France

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Journal of Mathematical Neuroscience - recent articles
by Stephen Coombes July 18, 2014

July 18, 2014

Dear all, The Journal of Mathematical Neuroscience publishes research articles on the mathematical modeling and analysis of all areas of neuroscience. The current list of journal articles is available at http://www.mathematical-neuroscience.com/ : Frequency Preference Response to Oscillatory Inputs in Two-dimensional Neural Models: A Geometric Approach to Subthreshold Amplitude and Phase Resonance Rotstein HG http://www.mathematical-neuroscience.com/content/4/1/11 Network Symmetry and Binocular Rivalry Experiments Diekman CO and Golubitsky M http://www.mathematical-neuroscience.com/content/4/1/12 Effects of Synaptic Plasticity on Phase and Period Locking in a Network of Two Oscillatory Neurons Akcay Z, Bose A and Nadim F http://www.mathematical-neuroscience.com/content/4/1/8 Approximate, not Perfect Synchrony Maximizes the Downstream Effectiveness of Excitatory Neuronal Ensembles Börgers C, Li J and Kopell N http://www.mathematical-neuroscience.com/content/4/1/10 Identification of Criticality in Neuronal Avalanches: II. A Theoretical and Empirical Investigation of the Driven Case Hartley C, Taylor TJ, Kiss IZ, Farmer SF and Berthouze L http://www.mathematical-neuroscience.com/content/4/1/9 All articles are Open Access. Best regards, Steve ------------------------------------------------------- Stephen Coombes Professor of Applied Mathematics School of Mathematical Sciences Nottingham, UK Tel: 0115 846 7836 http://www.maths.nott.ac.uk/~sc/ ------------------------------------------------------- This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Post-doc openings for theoretical neuroscience at UCSF and UCB
by Friedrich Sommer July 18, 2014

July 18, 2014

Post-doctoral fellow in computational/theoretical neuroscience The Chang Lab at UCSF and the Sommer Lab at UCB are jointly seeking two (2) post-doctoral fellows in computational/theoretical neuroscience. Our groups are developing and applying novel computational methods to understand population neural data. The positions have the specific focus on understanding the dynamics of neural population data collected directly from the cortical surface of humans during the perception and production of speech at multiple temporal resolutions. These positions are fully funded as part a collaborative effort between University of California San Francisco, University of California Berkeley, and Lawrence-Berkeley National Laboratory. This Bay Area collaboration combines UCSF's strong clinical and experimental neuroscience experience with in vivo cortical electrophysiology, UCB's expertise in theoretical neuroscience, statistical learning and data analysis, and LBNL's supercomputing and applied mathematics together with electronics and microfabrication. Successful applicants will have access to the full range of facilities and expertise uniquely allowed by this collaboration. Applicants should have a Ph.D. (or equivalent degree) in a quantitative field such as computer science, electrical engineering, physics, or applied mathematics/statistics with a strong publication record. Expertise in theoretical/computational neuroscience or the analysis/modeling of complex dynamical systems is recommended; experience in analyzing the dynamics of population neural recordings is preferred. Applicants must be able to work in a collaborative, multi-disciplinary environment and exhibit good communication skills. Experience with scientific programing languages (e.g. C/C++, python, Matlab) is required. Expertise in speech/language and/or high-performance computing is not required, but is beneficial. To apply, please submit a CV and three letters of reference to: changed(a)neurosurgery.ucsf.edu fsommer(a)berkeley.edu ----------------------------------------------------------------------------------------------------------------- Friedrich T. Sommer, Ph.D, Adjunct Professor Redwood Center for Theoretical Neuroscience & Helen Wills Neuroscience Institute UC Berkeley 575A Evans Hall, MC #3198 Berkeley, CA 94720-3198 http://redwood.berkeley.edu/wiki/Fritz_Sommer -----------------------------------------------------------------------------------------------------------------

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Neurocomputing special issue CFP
by Zhijun Yang July 17, 2014

July 17, 2014

Dear Colleagues, May we draw your attention to a Neurocomputing special issue CFP: Advances on Biological Rhythmic Pattern Generation: Experiments, Algorithms and Application. The full announcement can be found as an internet link below. http://www.journals.elsevier.com/neurocomputing/call-for-papers/special-iss… Instructions for submission: • The submission website for Neurocomputing is located at: http://ees.elsevier.com/neucom/default.asp • To ensure that all relevant manuscripts are correctly identified for inclusion into this special issue, it is important that authors select SI: Creating Biology Rhythm when reaching the “Article Type” step in the submission process. We look forward to receiving your contributions to what promises to be an exciting special issue. Best regards, Zhijun Yang -- Zhijun Yang, BEng, MSc, PhD, Lecturer in Design Engineering Department of Design Engineering and Mathematics School of Science and Technology Middlesex University, London NW4 4BT, UK Voice: +44 (0)7882681333 --------------------------------------------------------------------------- Please note that Middlesex University's preferred way of receiving all correspondence is via email in line with our Environmental Policy. All incoming post to Middlesex University is opened and scanned by our digital document handler, CDS, and then emailed to the recipient. If you do not want your correspondence to Middlesex University processed in this way please email the recipient directly. Parcels, couriered items and recorded delivery items will not be opened or scanned by CDS. There are items which are "exceptions" which will be opened by CDS but will not be scanned a full list of these can be obtained by contacting the University.

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Postdoc position in neural inspired computation
by Aimone, James Bradley July 17, 2014

July 17, 2014

A postdoctoral research position is available for research on neural algorithm development for a neural-inspired computing hardware project within the cognitive modeling group at Sandia National Laboratories. The successful applicant will join a broad interdisciplinary team that includes computational neuroscientists, computer scientists, and electrical engineers focused on developing methods for hardware acceleration of neural algorithms. He or she will be expected to leverage research from the broader neuroscience research community to develop computational approaches for addressing real-world problems. Previous experience both in neuroscience research and in data analytics / machine learning domains is ideal. For more information, please contact Dr. Brad Aimone (technical contact, jbaimon(a)sandia.gov<mailto:jbaimon@sandia.gov> ) or Dr. John Wagner (department manager, jswagne(a)sandia.gov<mailto:jswagne@sandia.gov>). For the full posting, necessary qualifications and application information, go to careers.sandia.gov and search for posting ID 646640 -------------------------- James Bradley Aimone, Ph.D. Senior Member of Technical Staff Cognitive Modeling Department Sandia National Laboratories Phone: (505) 284-3147 Fax: (505) 844-4728

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Research Specialist position at Princeton University
by Francisco Pereira July 16, 2014

July 16, 2014

A Research Specialist position is available in Matthew Botvinick's lab in the Princeton Neuroscience Institute, in collaboration with Francisco Pereira at Siemens Corporate Technology. This is a position within a team participating in the IARPA Knowledge Representation in Neural Systems program. The goal of the program is to develop models of how the brain represents conceptual knowledge, and how that knowledge is used when carrying out tasks like reading a sentence. These models will be tested using brain imaging data. The main role in this position is as a programmer writing the code needed to build such models, while also being involved in experiment design and data analysis. Examples of tasks you might be asked to do: - prepare text corpora for use in developing models - implement evaluation tasks that the models developed will be benchmarked with - collect material from online resources and behavioral experiments - prepare stimuli for brain imaging experiments or model building - help in designing and carrying out brain imaging and behavioral experiments - analyze behavioral and brain imaging experimental data It is an unusual position in that you will be gaining experience in both machine learning and cognitive neuroscience. In addition to the core research goals, we will also be delivering a concrete system to the funding agency, and hence this will be a fast-paced project. You will be working directly with the PIs and also graduate students and research scientists in the team. Essential qualifications are experience developing software in MATLAB or Python (Perl is also useful), as well as an undergraduate degree in computer science, biomedical engineering, cognitive neuroscience or a related field. Preferred qualifications are knowledge in natural language processing, machine learning, and collection, preprocessing and analysis of brain imaging data (e.g. SPM, FSL or AFNI). The final candidate will be required to pass a background check successfully. This is a 1 year position, starting as soon as possible, with an additional year possible contingent on funding availability and performance. To apply, please go to https://jobs.princeton.edu/applicants/jsp/shared/Welcome_css.jsp and use “Search Open Positions” with requisition number 1400452. Please email francisco.pereira(a)gmail.com with any pre-application inquiries.

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1st Call for Abstracts for the 7th Int'l Workshop on Guided Self-Organisation (Freiburg, Dec 16-18, 2014)
by Joschka Boedecker July 16, 2014

July 16, 2014

<apologies for possible cross-posting> Dear colleagues, This is an announcement and Call for Abstracts for the Seventh International Workshop on Guided Self-Organisation (GSO-2014) to be held from December 16-18, 2014 in Freiburg, Germany. http://ml.informatik.uni-freiburg.de/events/gso14/index The workshop will bring together researchers from a richly diverse background who share interest in understanding and designing self-organising systems. Of particular interest are well-founded, but general methods for characterizing such systems in a principled way with the view of ultimately allowing them to be guided toward prespecified goals. Information theory, nonlinear dynamics and graph theory are core to many of these methods, and quantifying complexity and its sources is a common theme. This year, the workshop is organised in collaboration with the BrainLinks-BrainTools cluster of excellence at University of Freiburg ( https://www.brainlinks-braintools.uni-freiburg.de/ ), and one focus theme will be guided self-organisation in neural systems. Submissions to the workshop are extended abstracts (one-two pages). If interested in participating, send an extended abstract (by September 7th, 2014) by email to: jboedeck at informatik dot uni-freiburg dot de The notifications are expected by September 21st, 2014. Authors of accepted submissions will present the content to the workshop (scheduled 30 minutes presentation). It is expected that post-workshop publication of selected papers will follow in a special journal issue (as has been the case for previous GSO workshops). Please consult the website above and also http://guided-self.org/ for more information. Best wishes, Joschka Boedecker Mikhail Prokopenko Martin Riedmiller

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Two Postdoctoral Positions in Computational Modeling of Primate Motor Control
by Yaroslav Molkov July 15, 2014

July 15, 2014

Two postdoctoral/research associate positions in computational neuroscience for the duration of up to three years are 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 and have excellent C++ programming skills. Previous experience in computational neuronal modeling is a plus. Interested candidates are encouraged to contact Dr. Rybak (rybak(a)drexel.edu) or 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. Drs. Rybak and Molkov will be available to answer questions and discuss this job opportunity with potential candidates at the CNS’2014 meeting in Quebec City, Canada (July 26-31). ================================= Ilya A. Rybak, Ph.D. Professor Department of Neurobiology and Anatomy Drexel University College of Medicine 2900 Queen Lane Philadelphia, PA 19129, USA Tel.: (215) 991-8596 FAX: (215) 843-9082 E-mail: rybak(a)drexel.edu Yaroslav Molkov, Ph.D. Assistant Professor Indiana University - Purdue University 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

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Linking Brain Models and Data: An Invitation from James Bonaiuto and Michael A. Arbib
by James Bonaiuto July 15, 2014

July 15, 2014

The USC Brain Project has just released a new version of their neuroinformatics tool, the Brain Operation DataBase (BODB) v4.0. BODB is a tool for modelers and experimentalists to document computational models of the brain and their linkages to summaries of experimental data. Models can be compared in terms of these relations, and experimental data summaries can be visualized in a variety of ways. Groups of users can build collaboratory workspaces which allow them to share groups of models and data and work together to develop new models. This latest version of BODB includes many new features: - Improved search functionality: users can now search federated databases such as CoCoMac (macaque neural connectivity) and Brede (human brain imaging) directly as well as use boolean combinations of search terms - Users can now maintain a list of their favorite entries outside any workspace - Model and BOP diagrams: users can generate clickable and zoomable graphs showing the relationships between brain operating principles (BOPs) and between models and summaries of empirical data (SEDs) - ERP SED visualization: users can view the locations of ERP components on a standard electrode placement system - Improved workspaces: workspaces now include an activity stream, discussion board, and bookmarks. Workspaces administrators can send invitations to other users to join the workspace. - ModelDB import: users can search ModelDB for models and import them to BODB for documentation of their linkage to SEDs - New Documentation System: the new system is far more extensive, is linked from pages on BODB, and users can now search the documentation - Web API: it is now possible to return BODB entries in JSON aand XML format through a simple URL protocol An overview of our general methodology for the neuroinformatics of brain modeling can be found at http://www.ncbi.nlm.nih.gov/pubmed/24234915. It is just one paper from a special issue of Neuroinformatics (Volume 12, Number 1, January 2014) on “Action, Language and Neuroinformatics” (Michael Arbib, Guest Editor). The Manual for BODB can be found at http://bodb.usc.edu/media/BODB_Manual.pdf. We invite you to register for a free account on BODB and add your own models and experimental data: http://bodb.usc.edu ------------------------------------------------------ James Bonaiuto, PhD Research Associate Sobell Department of Motor Neuroscience and Movement Disorders UCL Institute of Neurology 33 Queen Square, London WC1N3BG, United Kingdom

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2014 SFN Meeting Workshop: NSG Portal for parallel simulations
by Ted Carnevale July 14, 2014

July 14, 2014

What: Using the Neuroscience Gateway Portal for Parallel Simulations A Satellite Symposium at the 2014 Society for Neuroscience Meeting Where: Lodation to be announced in downtown Washington, DC When: 9 AM - Noon on Saturday, November 15, 2014 Speakers to include: A. Majumdar, S. Sivagnanam, and T. Carnevale Registration deadline: Friday, October 31, 2014 This workshop is intended for neuroscientists who are already using, or would like to use, the Neuroscience Gateway Portal (NSG http://www.nsgportal.org/) for parallel simulations. The NSG portal eliminates most administrative and technical barriers that face neuroscientists who need to use high performance computing resources for large modeling projects. Its web-based interface simplifies the tasks of uploading models, specifying job parameters, monitoring job status, and storing and retrieving output data. Simulators currently installed include Brian, MOOSE, GENESIS3, NEST, NEURON, and PyNN. The workshop will combine didactic presentations by NSG's developers, discussions with experienced users, and hands on instruction in how to use the portal. For more information and the online registration form see http://www.neuron.yale.edu/neuron/static/courses/nsg2014/nsg2014.html --Ted

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