- Comp-neuro - lists.cnsorg.org

2014 SFN Meeting Workshop: NSG Portal for parallel simulations
by Ted Carnevale Sept. 9, 2014

Sept. 9, 2014

What: Using the Neuroscience Gateway Portal for Parallel Simulations A Satellite Symposium at the 2014 Society for Neuroscience Meeting Where: Location 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 Do you have a large scale modeling project that exceeds the speed or capacity of your local hardware? Have you tried to use high performance computing (HPC) resources at your own institution, but found the process too difficult because of administrative or technical barriers? If yes, this workshop is for you. In a single morning session, you will learn how to use the Neuroscience Gateway Portal (NSG) http://www.nsgportal.org/ which is designed for neuroscientists who need to use HPC resources for large modeling projects. It simplifies every aspect of the process, from getting allocations of free CPU time to uploading your model, launching and monitoring jobs, and downloading results. The NSG already has several parallel simulators installed, including Brian, NEST, NEURON, PGENESIS and PyNN. Space is limited, so sign up quickly. See http://www.neuron.yale.edu/neuron/static/courses/nsg2014/nsg2014.html for further details and the registration form. Support: The NSG project is supported by a grant from the National Science Foundation. NSG provides its users free allocations of CPU time on HPC resources under the auspices of XSEDE (Extreme Science and Engineering Discovery Environment), which is also supported by NSF.

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PhD position in Neurocomputational modeling of language processing
by Hartmut Fitz Sept. 8, 2014

Sept. 8, 2014

A PhD position is available at the Max-Planck Institute for Psycholinguistics in Nijmegen, the Netherlands, within the 'Language in Interaction' consortium. The PhD candidate will participate in a team effort to understand the neurobiology underlying language processing by building computer models for sentence processing based on recurrent networks of spiking neurons. The goal is to develop a model with processing memory based on vector representations of words which are incrementally interpreted in terms of thematic roles ("who did what to whom"). A core objective will be to investigate the computational role of different neuronal models, connectivity types, neurobiologically motivated adaptation mechanisms, and different methods for calibrating the model's read-out units. Closing date: 30 September 2014 For more information see: https://www.languageininteraction.nl/jobs/phd-positions.html https://www.languageininteraction.nl/jobs/id-2nd-phd-call-general.html

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Postdoc opportunity at Stanford in Causal Brain Network Analysis
by Wei Wu Sept. 5, 2014

Sept. 5, 2014

Dear fellow researchers, The Etkin Lab at Stanford University is currently seeking to fill a postdoc position for causal brain network analysis. Please find below the job requirement and contact info. Thank you for your attention! Postdoc opportunity at Stanford in Causal Network Analysis – from Concurrent TMS/fMRI to Transdiagnostic Imaging of Psychiatric Disorders The Laboratory of Amit Etkin, MD PhD at Stanford University is currently accepting applications for a postdoctoral research fellowship focused on causal network analyses using fMRI in healthy individuals and patients with a range of psychiatric disorders. The focus of this position is on application of network analysis tools (e.g. graph theory, network-based statistics, etc) to fMRI data, including both causal circuit mapping experiments with concurrent transcranial magnetic stimulation (TMS) and fMRI, as well as resting-state data from patients across the mood, anxiety and stress disorders represented, and across the lifespan. The successful applicant will have a PhD in Cognitive Neuroscience, Neurophysiology, Psychology, Computer Science, Statistics or related fields. Experience with analysis of fMRI data or with causal network analysis tools is required. Additional programming experience is a plus. Duties will also include manuscript preparation, presentation of findings at conferences, management of research assistants and contribution to the preparation of grants. Laboratory and Stanford resources include research-dedicated 3T and 7T MRI scanners, concurrent TMS/fMRI setups and concurrent TMS/EEG setups. Salary commensurate with experience. More information about our ongoing studies can be found at: http://etkinlab.stanford.edu. To apply, please send a curriculum vitae, a statement describing research interests and relevant background and three letters of recommendations, as well as relevant reprints/preprints of research articles to: Amit Etkin, MD, PhD Department of Psychiatry and Behavioral Sciences Stanford University amitetkin(a)stanford.edu

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New software for neuronal model fitting
by Szabolcs Káli Sept. 5, 2014

Sept. 5, 2014

Dear Colleagues, We are pleased to announce the availability of the first public (beta) version of Optimizer, an interactive software tool for fitting the parameters of neuronal models. Optimizer was developed in Python, and has the following main features: - efficiently fits the free parameters of arbitrary neural (or other) models using advanced nonlinear optimization algorithms - all aspects of the optimization problem (including the model, its free parameters, the target data, the simulation and recording protocol, the error function) and the fitting process itself can be conveniently controlled from a graphical user interface (GUI) - full internal support for models implemented in the Neuron simulator (while other models can be also optimized using a "black box" approach) - choice of 7 different (tunable) optimization algorithms, including a customized evolutionary (genetic) algorithm, differential evolution, simulated annealing, the basinhopping algorithm, random search, and two local search methods - choice of 11 different error functions for the comparison of simulated and experimental (target) data, including generic ones as well as several feature-based ones which are appropriate for the comparison of membrane potential traces containing action potentials; error functions can be combined with arbitrary weights - the software is easily extensible in various ways to support novel scenarios A paper describing the software, several use cases, and comparisons with other model fitting tools, has been recently published in Frontiers in Neuroinformatics (the abstract and citation details are included at the end of this message): http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00063/abstract The software can be downloaded using git from https://github.com/vellamike/optimizer where you can also find instructions for installing the software and its dependencies. The current version of Optimizer has been verified to work under several recent Linux distributions. Alternatively, a compressed archive containing the software and various examples can be downloaded from https://github.com/vellamike/optimizer/releases/tag/v2.0-beta The documentation of the software is available at http://optimizer.readthedocs.org/en/latest/ Finally, we wish to encourage everyone interested in fitting neuronal models to try the software and provide feedback. If you find that your favorite optimization algorithm or error function is not currently included in Optimizer, it can probably be added with relatively little effort, especially given an existing implementation of the algorithm or function itself, and we would be very interested in collaborating on such an extension. We are also interested in learning about the model fitting problems encountered by potential users; we would be happy to advise users on whether and how Optimizer may be used to solve particular problems; in addition, future development of the software will be guided by the feedback that we receive. Best regards, Szabolcs Káli and Péter Friedrich Friedrich P, Vella M, Gulyás AI, Freund TF and Káli S (2014) A flexible, interactive software tool for fitting the parameters of neuronal models. Front. Neuroinform . 8 :63. doi: 10.3389/fninf.2014.00063 Abstract: The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool.

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Job/Fellowship Opportunity: Big Data IT Management and Automation in NeuroMorpho.Org
by Rubén Armañanzas Sept. 4, 2014

Sept. 4, 2014

George Mason University, Krasnow Institute for Advanced Study in Fairfax, VA (USA), invites applications for a full-time doctoral student graduate research assistant position available immediately in the Center for Neural Informatics, Structures, and Plasticity (krasnow1.gmu.edu/cn3) headed by Prof. Giorgio Ascoli. To be considered for this position, applicants must apply to the PhD program in Bioengineering at George Mason University (http://volgenau.gmu.edu/doctoral-degrees) following the instructions below. The successful applicant will join a collaborative multidisciplinary team at the cutting edge of the development and dissemination of digital tools and resources for neuroscience. The Ascoli Lab is funded by the National Institutes of Health, the National Science Foundation, the Office of Naval Research, the Air Force Office of Scientific Research, the Intelligence Advanced Research Projects Activity, and Keck. This position is particularly suited for computationally minded researchers seeking exposure to the burgeoning field of big data in neuroinformatics. The candidate will join the NeuroMorpho.Org project -- a free, public, centralized repository of neuronal digital reconstructions. NeuroMorpho.Org has firmly established itself as a powerful resource for the neuroscience community, with millions of downloads and data usage in over 200 publications by other labs since its 2006 public release. Its version 5.7 contains over 148,000 internal data files pertaining to more than 11,000 neuronal reconstructions contributed by 144 laboratories worldwide from 24 species and 95 brain regions. The pre-doctoral fellow will work within the CN3 research group and will be tasked with a variety of activities including design of new Information Technology (IT) solutions to enhance the performance of existing software and hardware infrastructure. Due to the growing pace of the field, the recipient will be also responsible for tuning and implementing the next generation support for Big Data handling of digital neuronal reconstructions. Desired qualifications include: 1. proficiency in C/C++, Java and Python; 2. experience in Unix/Linux server administration; MySQL design and administration; web technologies and API web services; content management systems; and 3. a BS/MS in Computer Science, Information/Systems/Software Engineering or a similar field. Knowledge in task analysis automation and interest in neuroscience are a plus. The position includes a $22,000/year 12 months-stipend (20 hours/week during academic year, 40 hours/week during summer) in addition to health insurance and up to 18 credits per year of tuition coverage in the Volgenau school of Engineering. To apply, please follow the PhD application instructions (http://volgenau.gmu.edu/how-to-apply) Include the wording "/Neuroinformatics fellowship in Prof. Giorgio Ascoli's lab/" in both your research/interest statement and cover letter. After submitting the application material, please also forward a copy of your resume, research/interest statement, and cover letter directly to ascoli(a)gmu.edu <mailto:ascoli@gmu.edu> with subject "Bioengineering PhD candidate". Beyond the frontiers of neuronal types

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Postdoctoral position at the University of Pittsburgh
by Brent Doiron Sept. 3, 2014

Sept. 3, 2014

Applications are invited for a Simons foundation funded postdoctoral position(s) in the Mathematics and Neuroscience departments of the University of Pittsburgh. The project will involve the collection, analysis, and modeling of large-scale multi-unit recordings from cortex, with an emphasis on understanding how visual attention modulates neural response. Of specific interest is elucidating the neural mechanisms that underlie the control of neural variability, as well as its consequences on neural function. Successful candidates will either be members of the working group of Dr. Brent Doiron and will be in tight collaboration with the Dr. Marlene Cohen, or vice versa, depending on the fit of the applicant. Theoretical candidates should expect to be members of the Doiron group, while candidates with an experimental focus would be in the Cohen group. Please visit www.math.pitt.edu/~bdoiron and www.cohenlab.com for a list of recent work from the Doiron and Cohen groups. The successful candidate(s) will be integrated into the Center for the Neural Basis of Cognition (http://www.cnbc.cmu.edu) a large and vibrant community of neuroscientists spanning many departments across the University of Pittsburgh and Carnegie Mellon University. The position is funded for several years, with an initial one-year appointment and an expectation of extension to at least three years, given satisfactory performance. The salary is competitive, and the start date is negotiable (January 2015 is optimal). Applicants with a PhD in Mathematics, Applied Mathematics, Neuroscience, Statistics, Biology, Psychology or a related discipline, and ideally with experience in computing, computational neuroscience, statistical analysis, or in vivo recording should send a CV including a list of publications, a research statement, and reference contact information to bdoiron(a)pitt.edu The University of Pittsburgh is an Affirmative Action, Equal Opportunity Employer, and women and members of minority groups under-represented in academia are especially encouraged to apply. -- Associate Professor of Mathematics Center for the Neural Basis of Cognition University of Pittsburgh 301 Thackeray Hall Pittsburgh, PA, 15260 www.math.pitt.edu/~bdoiron

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Tenure Track Faculty Position in Neuroscience at Rutgers University - Newark
by Bart Krekelberg Sept. 3, 2014

Sept. 3, 2014

The Center for Molecular & Behavioral Neuroscience (CMBN) at Rutgers University seeks outstanding candidates for a tenure track Assistant Professor position in NEUROSCIENCE. Applicants should hold a Ph.D. degree in Neuroscience or a related field and have completed at least two years of post-doctoral training. The ideal candidate for this position asks fundamental hypothesis-driven questions about brain structure and function and is open to establishing collaborative research efforts within the Rutgers neuroscience community. Research areas of particular interest are executive control, sensory-motor integration, learning and memory, and emotional regulation. The successful applicant will likely use a broad range of experimental approaches in non-human primates, humans, and/or rodents, and methods including electrophysiology, optogenetics, and functional imaging. The assistant professor will be expected to maintain an active externally-funded research program, to teach undergraduate and graduate courses in neuroscience, and to mentor Ph.D. students in the Behavioral and Neural Sciences program. Rutgers, The State University of New Jersey, is a leading national public research university and the state's preeminent, comprehensive public institution of higher education. Rutgers is dedicated to conducting research that breaks new ground; to teaching that meets the highest standards of excellence; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live. CMBN is located in Newark NJ, a short drive from New York City. CMBN is part of a large community of neuroscientists at Rutgers Newark, with additional researchers in the Departments of Biological Sciences and Psychology as well as in the Rutgers University New Jersey Medical School. Collectively, these researchers represent all levels of analysis in neuroscience (http://www.neuroscience.newark.rutgers.edu) Applicants should apply as soon as possible, but no later than 10/20/2014. Rutgers is an Equal Opportunity/Affirmative Action Employer and has a strong commitment to diversity. Women and members of underrepresented minorities are especially encouraged to apply. Rutgers-Newark is noted for its exceptionally diverse student population. To receive detailed instructions on how to apply, please send an email to search(a)cmbn.rutgers.edu with the subject line 'How to apply'. --- Bart Krekelberg, PhD Associate Director, Center for Molecular and Behavioral and Neuroscience Associate Director, Rutgers Brain Imaging Center Associate Professor, Rutgers University Newark, NJ 07102 USA T: 973 353 3602 W: vision.rutgers.edu E: bart(a)vision.rutgers.edu

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IWSYP’14 - I International Workshop on Synaptic Plasticity
by Thiago Matos Pinto Sept. 3, 2014

Sept. 3, 2014

Dear colleagues, Please see the information below about an upcoming workshop on synaptic plasticity. Best wishes, Thiago *** I International Workshop on Synaptic Plasticity - IWSYP’14 *** University of São Paulo, Ribeirão Preto, São Paulo State, Brazil Workshop dates: September 8th - 9th 2014 Organizers: Thiago Matos Pinto and Antonio Roque Participation is free of charge! This workshop is a satellite event of the XXXVIII Annual Meeting of the Brazilian Society for Neuroscience and Behavior (SBNeC), which will be held on September 10-13 in Búzios, Rio de Janeiro. The SBNeC meeting will also feature big names in Neuroscience, and will be a preparatory event for the 9th World Congress of the International Brain Research Organization (IBRO), which will take place in Rio de Janeiro in 2015. Confirmed speakers: Chris De Zeeuw (Erasmus Medical Center, Rotterdam, The Netherlands & Netherlands Institute for Neuroscience, Amsterdam, The Netherlands) Freek Hoebeek (Erasmus Medical Center, Rotterdam, The Netherlands) Reinoud Maex (École Normale Supérieure, Paris, France) Ricardo Leão (University of São Paulo, Ribeirão Preto, Brazil) Thiago Matos Pinto (University of São Paulo, Ribeirão Preto, Brazil) Gabriela Antunes (University of São Paulo, Ribeirão Preto, Brazil) Giseli de Sousa (Federal University of Santa Catarina, Florianópolis, Brazil) Cleiton Lopes Aguiar (University of São Paulo, Ribeirão Preto, Brazil) Renan Oliveira Shimoura (University of São Paulo, Ribeirão Preto, Brazil) Bruna Lanzillotta de Mattos (Fluminense Federal University, Niterói, Rio de Janeiro State, Brazil) Luana Chagas (Fluminense Federal University, Niterói, Rio de Janeiro State, Brazil) Querusche Zanona (Federal University of Rio Grande do Sul, Brazil) Fabiana Santana (Federal University of Rio Grande do Sul, Brazil) We look forward to seeing you in Ribeirão Preto. With best wishes, Thiago Matos Pinto, IWSYP'14 Organizer

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Faculty positions in Computer Science at American University
by Mark Laubach Sept. 2, 2014

Sept. 2, 2014

American University, College of Arts & Sciences, Department of Computer Science Computer Science (Assistant, Associate or Full Professor) The Department of Computer Science in the College of Arts and Sciences at American University in Washington, DC invites applications for up to three tenure-track or tenured Assistant/Associate/Full Professors to form a collaborating research team. We seek either a group of researchers who will be hired together, or a senior individual with a vision for filling the other positions. The team’s research expertise may be in any area of computer science. Following the department’s strong recent hires in the interdisciplinary areas of computational neuroscience and persuasive gaming, the university seeks to build computer science’s core program areas, which may include algorithms and data structures, architecture, robotics, databases and information retrieval, human-computer interactions, numerical and symbolic computation, operating systems, programming languages, or software methodology and engineering. Preference will be given to teams or visions that contribute to more than one of the core program areas, and that contribute to the university’s capacity in the area of big data. The Computer Science Department is currently in a period of expansion, and is poised to become a leader in the university’s technology an innovation sectors. To support this trajectory, the department will soon be moving to a new building that is designed to promote inspiration, collaboration, creation and cultivation. QUALIFICATIONS All applicants should have a strong record of (or potential for) externally sponsored research. We are especially eager to recruit candidates with established research partnerships (or the ability to form such partnerships) in the Washington, DC area. Candidates should also have a record of excellence in teaching and mentoring students. Teaching responsibilities will include core courses in computer science and more advanced courses in the applicant’s area of specialty. The Ph.D. in Computer Science or a closely related field is required; post-doctoral or industry experience is preferred. At least one appointment will be at a senior level with tenure. Preference will be given to senior candidates who are able and willing to lead the department, including (but not limited to) the development of a Ph.D. granting program. APPLICATION INSTRUCTIONS Applicants should include a statement (a joint statement for team applications) of research outlining the research focus (or foci) and future plans for developing a nationally competitive, externally funded research program at American University. In addition to a (joint, if applicable) research statement, each applicant should include statements of individual research and teaching experience, a CV, and the names of three references not in the proposed team. Please submit applications via: http://apply.interfolio.com/25813. Review of applications will begin November 3 and continue until the position is filled.

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Postdoc position available
by Olaf Sporns Sept. 2, 2014

Sept. 2, 2014

*Computational Cognitive Neuroscience Lab - Indiana University* *Postdoctoral Fellowship* Applications are invited for an open position as postdoctoral fellow in the Computational Cognitive Neuroscience Lab, Department of Psychological and Brain Sciences, Indiana University Bloomington. The core research focus of the lab is in the area of brain networks and connectomics. The lab works on anatomical and functional data sets from a number of species, with a strong emphasis on human brain connectivity and connectome data. Ongoing projects in the lab involve applications of models and tools from network science, graph theory, complex dynamics and information theory to basic and clinical/translational neurobiological questions. A description of the lab and current research areas can be found at www.indiana.edu/~cortex <http://www.indiana.edu/%7Ecortex> . Applicants should (a) have (or be in the final stages of obtaining) a PhD or equivalent degree in a field relevant to the research focus of the lab (e.g. neuroscience, neuroimaging, applied mathematics, computer science or bioengineering); (b) have a strong background in computational methods and programming (including advanced skills in Matlab); and (c) have strong enthusiasm for using computational approaches to understand neurobiological problems. Candidates with background in networks or graph theory, experience in processing and analyzing neuroimaging or electrophysiological recordings, exposure to "big data" approaches relevant to brain function, and a strong record of publication are especially encouraged to apply. The postdoctoral fellow will join a very active and interdisciplinary research group, and will be expected to engage and interact with a growing number of network and complex systems scientists at Indiana University and beyond. The lab maintains close ties and collaborations with scientists in the IU Imaging Research Facility (housing a 3T Siemens MR scanner), the Center for Complex Networks and Systems at the School of Informatics and Computing, the Medical School campus, and at other institutions nationally and internationally. All lab members have access to excellent computational facilities. The potential start date is negotiable, and the position is initially offered for a 1-year term which is renewable upon mutual agreement.Salary levels will follow NIH guidelines. Please email application materials (cover letter, a full CV with a list of publications, and 3 letters of reference) to Olaf Sporns at osporns(a)indiana.edu <mailto:osporns@indiana.edu> . -- Olaf Sporns -- @spornslab Department of Psychological and Brain Sciences Programs in Neuroscience and Cognitive Science Indiana University Bloomington, IN 47405

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