- Comp-neuro - lists.cnsorg.org

Linking Brain Models and Data: An Invitation from James Bonaiuto and Michael A. Arbib

by James Bonaiuto

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

July 15, 2014

2014 SFN Meeting Workshop: NSG Portal for parallel simulations

by Ted Carnevale

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

July 14, 2014

NEURON course at 2014 SFN Meeting

by Ted Carnevale

Using NEURON to Model Cells and Networks Satellite Symposium, Society for Neuroscience Meeting 9 AM - 5 PM on Friday, November 14, 2014 Speakers include Ted Carnevale, Bill Lytton, and Gordon Shepherd This course emphasizes practical issues that are key to the most productive use of NEURON, an advanced simulation environment for realistic modeling of biological neurons and neural circuits. Through lectures and live computer demonstrations, we will address topics that include the following: Partial list of topics that will be covered: * Efficient design and implementation of models of neurons and networks. * Constructing and managing models with NEURON's GUI, hoc, and Python. * Using the built-in variable-order variable-timestep integrator for improved speed and accuracy. * Parallelizing models of cells and networks to take advantage of multicore PCs and Macs, workstation clusters, and parallel supercomputers. * Expanding NEURON's repertoire of biophysical mechanisms, including an introduction to using the new RxD feature to implement models that involve reactive diffusion. * Databases for empirically-based modeling. Each registrant will receive a comprehensive set of notes. Registration is limited to 25 individuals on a first-come, first-serve basis. The registration deadline is Friday, October 31, 2014. NO on-site registration will be accepted. For more information and the online registration form, see http://www.neuron.yale.edu/neuron/static/courses/dc2014/dc2014.html --Ted

July 14, 2014

PhD open positions on event-driven robotics

by Chiara Bartolozzi

There are few PhD positions with scholarship for developing event-driven sensors and computation for the humanoid robot iCub at the Italian Institute of Technology. The call, application form and tips on the documentation to send are at the following link: http://www.iit.it/en/openings/phd-calls/2030-phd-course-topic-information.h… 1. Event-driven vision sensors for humanoid robots Tutors: Chiara Bartolozzi Department: iCub Facility (Istituto Italiano di Tecnologia) http://www.iit.it/en/research/departments/icub-facility.html Description: Carrying out real-world tasks robustly and efficiently is one of the major challenges of robotics. Biology clearly outperforms artificial computing and robotic systems in terms of appropriateness of the behavioural response, robustness to interference and noise, adaptation to ever changing environmental conditions, or energy efficiency. All these properties arise from the characteristics of the radically different style of sensing and computation used by the biological brain. In conventional robots, sensory information is available in a sequence of static frames and high dynamics can be sensed only by increasing the sampling rate. Unfortunately the available bandwidth limits the amount of information that can be transmitted forcing a compromise between resolution and speed. The goal of the proposed theme is the development of bio-inspired event-driven artificial vision sensors that will be mounted and validated on the humanoid robot iCub. The goal is to convey to the robot the most informative signal that it can use to robustly interact with the world. The research will focus on the design of mixed-mode analog/digital circuits for photo-transduction and focal-plane processing. Different architectures and circuits will be considered for the pixel design, evaluating the trade-off between complexity (and fill-in factor) and sensor pre-processing capabilities. Additionally, ad hoc digital asynchronous logic circuits and interfaces based on the "Address Event Representation" protocol will be developed for optimally interfacing the sensor with the robot. Requirements: degree in Electronic Engineering, Physics (or equivalent) and background in Analog and/or Digital Circuit Design, possibly on FPGA programming (VHDL, Verilog). High motivation to work on a robotic platform. Reference: C. Posch, D. Matolin, and R. Wohlgenannt, "A QVGA 143 dB Dynamic Range Frame-Free PWM Image Sensor With Lossless Pixel-Level Video Compression and Time-Domain CDS," IEEE J Solid-State Circuits, vol. 46, no. 1, pp. 259-275, Jan. 2011 Contacts: chiara.bartolozzi(a)iit.it<mailto:chiara.bartolozzi@iit.it> 2. Building the neuromorphic iCub Tutors: Chiara Bartolozzi Department: iCub Facility (Istituto Italiano di Tecnologia) http://www.iit.it/en/research/departments/icub-facility.html Description: Carrying out real-world tasks robustly and efficiently is one of the major challenges of robotics. Biology clearly outperforms artificial computing and robotic systems in terms of appropriateness of the behavioural response, robustness to interference and noise, adaptation to ever changing environmental conditions, or energy efficiency. All these properties arise from the characteristics of the radically different style of sensing and computation used by the biological brain. In conventional robots, sensory information is available in a sequence of static snapshots and high dynamics can be sensed only by increasing the sampling rate. Unfortunately the available bandwidth limits the amount of information that can be transmitted forcing a compromise between resolution and speed. The goal of the proposed theme is the integration of event-driven sensors and computing platforms on the humanoid robot iCub. The goal is to convey to the robot the most informative signal that it can use to robustly interact with the world and provide adequate computing platforms such as the SpiNNaker system. The research will focus on the development of the infrastructure for optimally interfacing event-driven hardware modules based on the Address Event Representation protocol on the iCub. Requirements: degree in Electronic Engineering, Physics (or equivalent) and background on FPGA programming (VHDL, Verilog). High motivation to work on a robotic platform. Reference: C. Bartolozzi, F. Rea, C. Clercq, M. Hofstätter, D. B. Fasnacht, G. Indiveri, and G. Metta, "Embedded neuromorphic vision for humanoid robots," in IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops (CVPRW), 2011, pp. 129-135 Contacts: chiara.bartolozzi(a)iit.it<mailto:chiara.bartolozzi@iit.it> 3. Event-driven vision for the iCub Tutors: Chiara Bartolozzi, Lorenzo Natale Department: iCub Facility (Istituto Italiano di Tecnologia) http://www.iit.it/en/research/departments/icub-facility.html Description: Interacting with a dynamical environment is one of the major challenges of robotics. Biology clearly outperforms robotic systems when acting in real scenarios in terms of appropriateness of the behavioural response, robustness to interference and noise, adaptation to ever changing environmental conditions, and energy efficiency. All these properties arise from the characteristics of the radically different style of sensing and computation used by the biological brain. In conventional robots, sensory information is available in a sequence of static snapshots and high dynamics can be sensed only by increasing the sampling rate. However the available bandwidth limits the amount of information that can be transmitted forcing a compromise between resolution and speed. Event-driven vision sensors transmit information as soon as a change occurs in their visual field, achieving incredibly high temporal resolution, coupled with extremely low data rate and automatic segmentation of significant events. The proposed theme aims at the exploitation of highly dynamical information from event-driven sensors for robust interaction of the humanoid robot iCub with moving objects. The goal is to develop new techniques for the recognition and prediction of trajectories of moving targets including humans and objects and plan for precise reaching movements, by exploiting the high temporal resolution and compressive signal encoding of event-driven vision sensors mounted on the iCub. The research will focus on the development of the infrastructure for handling event-driven sensory data and of event-driven vision algorithms for motion estimation as well as algorithms for trajectory prediction. Real time behaviour will be achieved by using compressive event driven computation and on-board processing on FPGA. Requirements: degree in Computer Science or Engineering (or equivalent) and background in Computer Vision and/or Machine Learning. High motivation to work on a robotic platform and good computer and FPGA programming skills Reference: Benosman, R.; Clercq, C.; Lagorce, X.; Sio-Hoi Ieng; Bartolozzi, C., "Event-Based Visual Flow," Neural Networks and Learning Systems, IEEE Transactions on , vol.25, no.2, pp.407,417, Feb. 2014, doi: 10.1109/TNNLS.2013.2273537 Contacts: chiara.bartolozzi(a)iit.it<mailto:chiara.bartolozzi@iit.it> , lorenzo.natale(a)iit.it<mailto:lorenzo.natale@iit.it> 4. New techniques for vision-assisted speech processing for the iCub Tutors: Chiara Bartolozzi, Leonardo Badino Department: iCub Facility (Istituto Italiano di Tecnologia) http://www.iit.it/en/research/departments/icub-facility.html Description: Robust speech detection in realistic environments for human robot interaction is still a challenging task. Vision is currently used for improving speech recognition in noisy acoustic environments, however, the temporal content of the visual information is severely limited by the temporal discretization of the frame-based acquisition. Event-driven vision sensors transmit information as soon as a change occurs in their visual field, achieving incredibly high temporal resolution, coupled with extremely low data rate and automatic segmentation of significant events. The goal of the proposed theme is the exploitation of highly dynamical information from event-driven vision sensors for robust speech processing for the humanoid robot iCub. The goal is to extract visual features and cues from the stream of visual events that are related to speech production landmarks and exploit them for further improving speech recognition. The research will focus on the development of the infrastructure for handling event-driven sensory data and of novel algorithms for extraction of visual features from event-driven cameras. Requirements: degree in Computer Science or Engineering (or equivalent) and background in Auditory Processing and/or Machine Learning. High motivation to work on a robotic platform and good computer and FPGA programming skills. Reference: G. Potamianos, C. Neti, G. Gravier, A. Garg, and A.W.Senior in Proceedings of the IEEE Vol. 91 No. 9 September 2003 pp. 1306-1326 Benosman, R.; Clercq, C.; Lagorce, X.; Sio-Hoi Ieng; Bartolozzi, C., "Event-Based Visual Flow," Neural Networks and Learning Systems, IEEE Transactions on , vol.25, no.2, pp.407,417, Feb. 2014, doi: 10.1109/TNNLS.2013.2273537 Contacts: chiara.bartolozzi(a)iit.it<mailto:chiara.bartolozzi@iit.it> , leonardo.badino(a)iit.it<mailto:leonardo.badino@iit.it> Chiara Bartolozzi Researcher Istituto Italiano di Tecnologia Via Morego, 30 16163 Genoa, Italy Ph: +39 010 7178-1474

July 14, 2014

Two Postdoctoral Positions in Computational Modeling of Primate Motor Control

by Yaroslav Molkov

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

July 13, 2014

Job offer in Juelich, Germany - IT-Solutions Architect (f/m)

by Martina Reske

The Institute of Neuroscience and Medicine (INM) investigates the structure and function of the brain. The department INM-6 is conducting research in the field of Computational and Systems Neuroscience with currently four work groups and one Helmholtz Young Investigator Group (www.csn.fz-juelich.de<http://www.csn.fz-juelich.de>). The Ju?lich Supercomputing Centre (JSC) as part of the Institute for Advanced Simulation (IAS) offers high performance computing resources for scientific and technical applications which are among the most powerful in Europe and worldwide. The Simulation Lab Neuroscience at JSC is dedicated to enabling and supporting the Computational Neuroscience community in leveraging these resources for their research. These institutes are jointly looking for an IT-Solutions Architect (f/m) Your Job: * Design and development of web solutions * Implementation of web sites on the basis of open source solutions (e.g., WordPress/MediaWiki) * Integration of own and third-party components into the web sites * Writing of scripts/programs (e.g. in Python) in a neuroscience environment * Interaction with scientists to find the optimal solution for different situations * Proactive updates and creation of content for web sites in the field of neuroscientific simulation software * Creation of documentation of simulation of software in collaboration with scientists * The successful candidate will work half-time for INM-6 and the Simulation Lab Neuroscience at JSC, respectively. Your Profile: * Completed training in mathematical-technical software development or Bachelor in the area of Computer Science or comparable qualification * Very good knowledge of the relevant web technologies: PHP, MySQL, (X)HTML, JavaScript, CSS * Experience with the administration of web servers under Linux (LAMP) Experience with a common content management system (e.g., WordPress, MediaWiki, Typo3) * Good knowledge of shell and scripting languages like bash and Python * Fluently spoken and written English * Background in neuroscience or another natural science would be a plus * Interest in working with an interdisciplinary team of researchers with highest scientific standards Our Offer: * A diverse range of activities in a creative, interdisciplinary, international team * Forschungszentrum Jülich offers an excellent scientific research infrastructure on a green campus close to Cologne, Düsseldorf and Aachen * Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD). Forschungszentrum Jülich aims to employ more women in this area and therefore particulary welcomes applications from women. We also welcome applications from disabled persons. We look forward to receiving your application, preferably online via our online recruitment system (see here: http://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2014-115-EN…) quoting the reference number 2014-115. Martina Reske -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

July 11, 2014

Job announcement

by Quel

[sorry for cross-posting] On the behalf of Hospital Israelita Albert Einstein, *Open position for Professor of Neurosciences in Sao Paulo, Brazil.* A full time endowed position for “Professor of Neurosciences” is available at the Brain Institute at the Albert Einstein Institute for Research and Education (InCe – IIEPAE), São Paulo, Brazil. We seek an outstanding senior researcher as a professor of the Institute. Job description The main goals include the development of research in neuroscience involving ageing processes in the brain and methods to promote healthy ageing. Additional focus includes study of neurodegenerative diseases. The position requires a record of scientific excellence and management experience, as well as vision and motivation to lead and shape a team of researchers. The candidate is expected to lead a strong, internationally competitive research programme, attract external funding and promote an interactive and synergistic research environment in order to develop clinical neuroscience into a center of excellence in biological aspects of ageing. Good communication skills are required to interact with a multidisciplinary team of experienced neurologists, neurosurgeons, scientists, engineers, physicists and psychologists. *Required skills/Qualifications* • Senior researcher with PhD • Experience working as a leading researcher • A strong track record of publications, ideally h-index > 20 Desired skills/Qualifications • MD title • Portuguese speaking *Salary* Salary is provided by a donation (equivalent to a top salary for a physician in Brazil USD120,000.00 – 180,000.00 per year). The position is renewable. The appointment is for 24 months at first. *About Hospital Israelita Albert Einstein* Hospital Israelita Albert Einstein ranks number one in Latin America, was the first hospital outside of USA accredited by the Joint Commission International and possesses a number of ISO certifications. The Brain Institute-IIEPAE has a state-of-the art whole body 3T MR system equipped with 32 channel head coil with protected time for research, integrated with a 64 channel EEG-fMRI system. The facilities also include an fMRI eye-tracking system, TMS and in house stimulus delivery systems for advanced applications. Radiopharmacy laboratories for basic research and clinical application, an experimental core facility with a cell culture laboratory and genome sequencing and an AAALAC certified experimental facility are also available. The institution also holds a postgraduate programme in health sciences, recognized by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES), giving the opportunity to supervise postdoc, PhD and master students. *Apply for position:* The position is open until 31st of July. The top 20 CV will be selected and evaluated by a committee. Please e-mail CV, NIH Biosketch, statement of research interests and contact information of references to: ince(a)einstein.br with “Professor of Neurosciences” in the subject line Brain Institute - Albert Einstein Jewish Institute for Education and Research Hospital Israelita Albert Einstein – www.einstein.br Phone: +55 11 2151-3727 Best regards, Anna *Anna Ringheim Cadete* Coordinator - Brain Institute - IIEP SBIB Hospital Albert Einstein

July 10, 2014

Job opening: 7 PhD positions in Dutch research consortium "Language in Interaction"

by Lorenz, C.M.

Seven PhD Positions in the Dutch Research Consortium 'Language in Interaction' Closing date: 30 September 2014 For more information: http://www.languageininteraction.nl/jobs/id-2nd-phd-call-general.html We are looking for highly motivated PhD candidates to enrich a unique consortium of researchers that aims to unravel the neurocognitive mechanisms of language at multiple levels. The goal is to understand both the universality and the variability of the human language faculty from genes to behaviour. The Netherlands has an outstanding track record in the language sciences. This research consortium sponsored by a large grant from the Netherlands Organization for Scientific research (NWO) brings together many of the excellent research groups in the Netherlands with a research programme on the foundations of language. The research team consists of 43 Principal Investigators. In addition to the excellence in the domain of language and related relevant fields of cognition, our consortium provides state-of-the-art research facilities and a research team with ample experience in the complex research methods that will be invoked to address the scientific questions at the highest level of methodological sophistication. These include methods from genetics, neuroimaging, computational modelling, and patient-related research. This consortium realizes both quality and critical mass for studying human language at a scale not easily found anywhere else. Currently, the consortium advertises seven PhD positions for a period of 4 years. Depending on the PhD position applied for, candidates will be appointed at one of the home institutions of the consortium. These positions provide the opportunity for conducting world-class research as a member of an interdisciplinary team. Click for more information on the PhD positions and how to apply: http://www.languageininteraction.nl/jobs/id-2nd-phd-call-general.html

July 10, 2014

Multiscale analysis of neural spike trains

by Reza Ramezan

Dear Colleagues, I would like to highlight the following paper from our group published in Statistics in Medicine (not a mainstream neuroscience journal). Interested people can receive a free (electronic) copy upon request. Kindest Regards, Reza Ramezan ------------------------------------------------------------------------------------ *Multiscale analysis of neural spike trains* <http://onlinelibrary.wiley.com/doi/10.1002/sim.5923/abstract> Ramezan R, Marriott P, Chenouri S (2014) *Summary:* This paper studies the multiscale analysis of neural spike trains, through both graphical and Poisson process approaches. We introduce the interspike interval plot, which simultaneously visualizes characteristics of neural spiking activity at different time scales. Using an inhomogeneous Poisson process framework, we discuss multiscale estimates of the intensity functions of spike trains. We also introduce the windowing effect for two multiscale methods. Using quasi-likelihood, we develop bootstrap confidence intervals for the multiscale intensity function. We provide a cross-validation scheme, to choose the tuning parameters, and study its unbiasedness. Studying the relationship between the spike rate and the stimulus signal, we observe that adjusting for the first spike latency is important in cross-validation. We show, through examples, that the correlation between spike trains and spike count variability can be multiscale phenomena. Furthermore, we address the modeling of the periodicity of the spike trains caused by a stimulus signal or by brain rhythms. Within the multiscale framework, we introduce intensity functions for spike trains with multiplicative and additive periodic components. Analyzing a dataset from the retinogeniculate synapse, we compare the fit of these models with the Bayesian adaptive regression splines method and discuss the limitations of the methodology. Computational efficiency, which is usually a challenge in the analysis of spike trains, is one of the highlights of these new models. In an example, we show that the reconstruction quality of a complex intensity function demonstrates the ability of the multiscale methodology to crack the neural code. *Keywords: *inhomogeneous Poisson process; multiscale analysis; periodogram; almost periodic intensity function; retinogeniculate synapse; spike train -- Reza Ramezan Department of Statistics and Actuarial Science University of Waterloo Waterloo, Ontario N2L 3G1 Canada Office: M3 3018 Phone: (519) 888-4567, ext. 39358 E-mail: rramezan(a)uwaterloo.ca Web: http://www.neuroinformatics.ca

July 9, 2014

2 PhD positions in Computational Neuroscience in Juelich, Germany

by Martina Reske

Dear community, we are seeking two PhD candidates to support our team! Project 1: In the framework of the Klinische Forschergruppe (KFO) 219 "Basal ganglia-cortex loops: Mechanisms of pathologic interactions and their therapeutic modulation" we have an open PhD student position in work package 9: "Mathematical modeling of development and suppression of pathological activation in basal ganglia – cortex loops“. This project focuses on the generation of pathological beta band oscillations in basal ganglia and their susceptibility to suppression by means of pharmacological challenges or deep brain stimulation. Specifically, this projects aims to model dynamics in basal ganglia – thalamus – cortex loops drawing on computational neuroscience approaches and data deriving from other work packages within the research consortium. We are seeking for a candidate with a master’s degree in physics, mathematics or computer science. The candidate will develop microscopic network models and will be supervised by the projects leaders, particularly by a postdoctoral fellow supervising the entire work package as well as Prof. Morrison. Programming expertise is appreciated. The candidate will be primarily based at the Jülich Research Center to foster interactions with theoretical neuroscientists. In addition, the candidate is expected to work jointly with project partners at the University Clinic of Cologne. We offer a position in a creative and international team, themes ranging from computational neuroscience to simulation technology. The Jülich Research Center is one of the largest research centers in Germany, with excellent scientific equipment, located on a green campus, and near the cultural centers Köln, Düsseldorf, and Aachen. The PhD position is available for 3 years, starting as soon as possible. Applications, including a motivation letter, CV, publication list, copies of university certificates, and one reference letter should be sent as a single PDF email attachment (max. 10MB) mentioning the internal reference code KFO219-TP9 to should be sent to: Dr. Martina Reske (m.reske(a)fz-juelich.de) – Scientific Coordinator The call is open until the position has been filled. Project 2: Project title: Neural circuit mechanisms of reinforcement learning Project description: Reinforcement learning is considered to play a major role in decision-making, and impairments in RL have been associated with various neuropsychiatric disorders including addiction and depression. Since it was found that the activity of midbrain dopamine (DA) neurons appears to represent the reward prediction error, various brain regions in the cerebral cortex and the basal ganglia have been shown to represent several variables appeared in mathematical formulations of RL algorithms. However, underlying mechanisms at the cellular and circuit levels within and between each of those regions remain largely unknown. In this project, we address this issue by developing and study neuronal network models of learning from reward and punishment in the brain's basal ganglia network. The project will be carried out by the group Functional Neural Circuits at the Institute for Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) led by Prof. Abigail Morrison, together with our Japanese collegues (Kenji Morita, University of Tokyo). The project is supported by German Ministry of Science (BMBF) in the framework of the German-Japan cooperation in Computational Neuroscience. The project incorporates tools and methods from different fields, ranging from neuroscience to physics and mathematical modeling to build large scale simulations of neural networks. Supervision is provided by Prof. Abigail Morrison and Dr. Jenia Jitsev, both having considerable experience in neural network modeling, with focus on plasticity and learning. We seek a highly motivated candidate with curiosity and persistence. A preferable candidate will have background and strong Master degree in either in neuroscience, physics, mathematics, biology, computer science or a related field of natural science. The candidate should have experience in basic software engineering techniques (minimal requirement is ability to write clear well-structured code in either C++ or Python). Furthermore, a solid basis in mathematical modelling (handling differential equations, basics of stability analysis) is essential. The most important requirement is the ability to learn new things and to find ways to solve novel problems. The PhD position is available for 3 years, starting as soon as possible. During the PhD, you will also have opportunity to visit conferences, workshops, summer schools and labs of our partners in Tokyo and benefit from their experience, too. You will be a part of a creative and young team, rich with inspiration for the different state-of-the art topics in experimental and theoretical neuroscience, and have the opportunity to take part at the forefront of current neuroscientific research. Research Center Jülich, Germany, is located on a green campus and hosts excellent facilities, including the Jülich Supercomputing Center, and is part of newly starting EU Human Brain Project, the largest neuroscientific initiative to study the brain funded in Europe. Jülich is close to large urban centers like Cologne, Aachen and Düsseldorf and offers thus a rich cultural environment to spend time in. Applications, including a motivation letter, a CV, copies of university certificates, and one letter of reference should be sent as a single PDF email attachment (max. 10MB) mentioning the internal reference code BRDJ-PhD to: Dr. Martina Reske (m.reske(a)fz-juelich.de) – Scientific Coordinator The call is open until the position has been filled. -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

July 9, 2014