- Comp-neuro - lists.cnsorg.org

Allen Institute Modeling Software Workshop
by Anton Arkhipov Jan. 4, 2023

Jan. 4, 2023

Happy New Year, everyone! Please join us for the Allen Institute Modeling Software Workshop in beautiful Seattle, on July 13-14, 2023! https://alleninstitute.org/what-we-do/brain-science/events-training/2023-mo… Sponsored by the NIH BRAIN program, this workshop is organized by the Allen Institute and our collaborators at the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. This 2-day in-person workshop will consist of interactive seminars and hands-on computational work. It will focus on teaching the skills for building and simulating complex and heterogeneous network models grounded in real biological data. The tools covered by the workshop include: * The SONATA file format<https://github.com/AllenInstitute/sonata> for multiscale neuronal network models and simulation output. * The Brain Modeling ToolKit (BMTK)<https://alleninstitute.github.io/bmtk/> – a Python-based software package for building and simulating network models at multiple levels of resolution. * The Visual Neuronal Dynamics (VND)<http://www.ks.uiuc.edu/Research/vnd/> – a program for displaying, animating, and analyzing neural network models using 3D graphics and built-in scripting. Workshop Topics: * Building heterogenous neural networks at different levels of resolution * Simulating networks of biophysically detailed, multi-compartmental neuronal models * Simulating networks of point-neuron models * Providing realistic spiking inputs to the neural networks * Simulating perturbations * Simulating extracellular electric field * Using and sharing models in the SONATA format * Visualizing network models’ structure and dynamics in 3D We are eager to host a diverse audience, and we encourage trainees, scientists, and PIs to apply. Prior experience in modeling is not required or expected. The Allen Institute strives to make training opportunities available on a fair and equitable basis. Some travel funding is available for participants with financial need. Please indicate on your application whether such support is needed. Applications will be evaluated on a need-blind basis. There is no fee to participate in the workshop. Applications are due on February 15. All applicants will be notified of the status of their application by April 15. See more information and apply here: https://alleninstitute.org/what-we-do/brain-science/events-training/2023-mo… Anton Arkhipov Associate Investigator T: 206.548.8414 E: antona(a)alleninstitute.org<mailto:antona@alleninstitute.org> [Text Description automatically generated] alleninstitute.org<https://alleninstitute.org> brain-map.org

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Modellers Workshop for the Brain Dynamics Toolbox
by Stewart Heitmann Jan. 3, 2023

Jan. 3, 2023

Modeller’s Workshop for the Brain Dynamics Toolbox. An online course for those who wish to simulate user-defined dynamical systems using the Brain Dynamics Toolbox (bdtoolbox.org<https://bdtoolbox.org>). This is a self-paced course with a practical focus on the art of programming differential equations. Video lectures guide the student through every step of building the model. Topics include Ordinary Differential Equations, Partial Differential Equations, Delay Differential Equations, Stochastic Differential Equations, Auxiliary Plot Functions and command-line tools. Example code is provided in all cases. Study time is 8 hours. Course Website https://bdtoolbox.teachable.com/p/modellers-workshop Reference Heitmann & Breakspear (2022) Handbook for the Brain Dynamics Toolbox: Version 2022. ISBN 978-0-6450669-2-0. Stewart Heitmann | Computational Scientist Victor Chang Cardiac Research Institute | Lowy Packer Building | 405 Liverpool St, Darlinghurst NSW 2010 Australia E: s.heitmann(a)victorchang.edu.au<mailto:s.heitmann@victorchang.edu.au> | @VictorChangInst Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.

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Postdoc position - Cheng Lab - Application deadline extended
by Vinita Samarasinghe Jan. 2, 2023

Jan. 2, 2023

*The application deadline for this position has been extended until 31.01.2023 * *Postdoctoral Position in Computational Neuroscience at the Institute for Neural Computation, Faculty of Computer Science* Prof. Sen Cheng, Institute for Neural Computation, Faculty of Computer Science at the Ruhr University Bochum, invites applications for a full time (currently 39.83 hours/week) *Postdoctoral position (TV-L E13) in Computational Neuroscience. * The position starts as soon as possibleand is funded until 30.06.2025. *Job description* The position is part of the Collaborative Research Center “Extinction Learning” (SFB 1280) and studies the principles underlying spatial learning and its extinction with reinforcement learning models. A particular focus is the role of episodic-like memory in learning and extinction processes. The research group is highly dynamic and uses diverse computationalmodeling approachesincludingbiological neural networks, cognitive modeling, and machine learning to investigatelearning and memory in humans and animals. For further information see www.rub.de/cns <http://www.rub.de/cns>. *Your Profile: * Candidates must have * a doctorate degreein neuroscience, physics, mathematics, electrical/biomedical engineering or a closely related field, * relevant experience in mathematical modeling, * excellent programming skills (e.g., Python, C/C++, Matlab), * excellent communication skills in English * the ability to work well in a team. Research experience in neuroscience would be a further asset. The Ruhr University Bochum is home to a vibrant research community in neuroscienceand cognitive science. The Institute for Neural Computation combines different areas of expertise ranging from experimental and theoretical neuroscienceto machine learning androbotics. Please send your application, including CV, transcripts and research statement electronically, as a *single PDF file*, to samarasinghe(a)ini.rub.de <mailto:samarasinghe@ini.rub.de>. In addition, at least two academic references mustbe sent independently to the above email address. The deadline for applications is January 31^st , 2023. Travel costs for interviews will not be reimbursed. The Ruhr University Bochum is committed to equal opportunity. We strongly encourage applications from qualified women and persons with disabilities. We are committed to providing a supportive work environment for female researchers, in particular those with young children. Our university provides mentoring and coaching opportunities specifically aimed at women in research. We have a strong research network with female role models and will provide opportunities to networkwith them. Wherever possible, events will be scheduled during regular childcare hours. Special childcare will be arranged if events have to be scheduled outside of regular hours, in case of sickness and during school or daycare closures. Where childcare is not an option parents will be offered a home office solution. Contact person: Vinita Samarasinghe, samarasinghe(a)ini.rub.de <mailto:samarasinghe@ini.rub.de> -- Vinita Samarasinghe M.Sc., M.A. Science Manager Arbeitsgruppe Computational Neuroscience Institut für Neuroinformatik Ruhr-Universität Bochum, NB 3/73 Postfachnummer 110 Universitätstr. 150 44801 Bochum Tel: +49 (0) 234 32 27996 Email:samarasinghe@ini.rub.de

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2x Funded PhD positions in Learning & Decision Neuroscience at the University of Birmingham, UK
by Lei Zhang Dec. 30, 2022

Dec. 30, 2022

--- Happy New Year & Apologize for cross-posting --- **2x Funded PhD positions in Learning & Decision Neuroscience at the University of Birmingham, UK** Dr. Lei Zhang (https://lei-zhang.net/) is looking for 2x PhD students interested in the cognitive, computational, and neural basis of (social) learning and decision-making in health and disease. The deadline for applications is in January 2023 to start in autumn 2023. The newly opened ALP(E)N Lab (Adaptive Learning Psychology and Neuroscience Lab) addresses the fundamental question of the “adaptive brain” by studying the cognitive, computational, and neurobiological basis of (social) learning and decision-making in healthy individuals (across the lifespan), and in psychiatric disorders. We combine an array of approaches including neuroimaging, patient studies and computational modelling (particularly hierarchical Bayesian modelling) with behavioural paradigms inspired by learning theories. The lab has a strong emphasis on equality, diversity and supporting lab members to thrive. The lab is based at the Centre for Human Brain Health ( https://birmingham.ac.uk/research/centre-human-brain-health/index.aspx) and Institute of Mental Health ( https://birmingham.ac.uk/research/mental-health/index.aspx) at the University of Birmingham, UK, with access to exceptional facilities including MRI, MEG, TMS, and fNIRS. Funding is available through two competitive schemes from the BBSRC ( https://www.ukri.org/councils/bbsrc/) and MRC ( https://www.ukri.org/councils/mrc/) that provide a stipend, fees (at UK rate) and a research allowance, amongst other benefits. International (ie, outside UK) applicants are welcome. The BBSRC project "Unravelling adaptive and flexible learning behaviour under social dynamics in health and disease" is in collaboration with Dr. Matthew Apps (Birmingham). Link to details: https://www.findaphd.com/phds/project/unravelling-adaptive-and-flexible-lea… The MRC Project "Neurocomputational mechanisms of self-referencing in social anxiety" is in collaboration with Dr. Patricia Lockwood (Birmingham), Dr. Mark Haselgrove (Nottingham) and Dr. Mona Garvert (London, as Industry Partner) Link to details: https://www.findaphd.com/phds/project/neurocomputational-mechanisms-of-self… Interested candidates should first send their CV and a short statement of research intentions by 9th January 2023 to Dr. Lei Zhang ( l.zhang.13(a)bham.ac.uk) before applying through the schemes, as only a small number of applicants can be put forward. Informal inquiries should also be directed to Dr. Lei Zhang. Many thanks, Lei Dr. Lei Zhang Principal Investigator/Associate Professor Centre for Human Brain Health & Institute for Mental Health School of Psychology University of Birmingham, UK e: l.zhang.13(a)bham.ac.uk w: lei-zhang.net t: @lei_zhang_lz

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Okinawa/OIST Computational Neuroscience Course 2023
by Erik De Schutter Dec. 26, 2022

Dec. 26, 2022

OKINAWA/OIST COMPUTATIONAL NEUROSCIENCE COURSE 2023 Methods, Neurons, Networks and Behaviors June 19 to July 6, 2023 Okinawa Institute of Science and Technology Graduate University, Japan https://groups.oist.jp/ocnc <https://groups.oist.jp/ocnc> The aim of the Okinawa/OIST Computational Neuroscience Course is to provide opportunities for young researchers with theoretical backgrounds to learn the latest advances in neuroscience, and for those with experimental backgrounds to have hands-on experience in computational modeling. We invite graduate students and postgraduate researchers to participate in the course, held from June 19th through July 6th, 2023 at an oceanfront seminar house of the Okinawa Institute of Science and Technology Graduate University. Applications are through the course web page (https://groups.oist.jp/ocnc <https://groups.oist.jp/ocnc>) only; January 1 - January 31, 2023. Applicants will receive confirmation of acceptance end of March. Like in preceding years, the 18th OCNC will be a comprehensive three-week course covering single neurons, networks, and behaviors with ample time for student projects. The first week will focus exclusively on methods with hands-on tutorials during the afternoons, while the second and third weeks will have lectures by international and local experts. The course has a strong hands-on component based on student proposed modeling or data analysis projects, which are further refined with the help of a dedicated tutor. Applicants are required to propose their project at the time of application. There is no tuition fee. The sponsor will provide lodging and meals during the course and may provide partial travel support. We hope that this course will be a good opportunity for theoretical and experimental neuroscientists to meet each other and to explore the attractive nature and culture of Okinawa, the southernmost island prefecture of Japan. Invited faculty: • Upinder Bhalla (NCBS, India) • Claudia Clopath (Imperial College London, UK) • Erik De Schutter (OIST) • Kenji Doya (OIST) • Tomoki Fukai (OIST) • Izumi Fukunaga (OIST) • Yukiko Goda (OIST) • Mike Häusser (University College London, UK) • Bernd Kuhn (OIST) • Jinny Kim (KIST, South Korea) • Rosalyn Moran (King's College London, UK) • Steve Prescott (University of Toronto, Canada) • Sam Reiter (OIST) • Greg Stephens (OIST) • Kazumasa Tanaka (OIST)

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TR: MSc internship offer (dynamical systems for neurosciences)
by DEPANNEMAECKER Damien Dec. 25, 2022

Dec. 25, 2022

MSc Internship Project: Dynamical study of a mean-field model of neural network activity driven by biophysical ion exchange mechanisms Project description. In neuroscience, the question of scales is central, ranging from the molecule to the whole brain. In theoretical and computational neuroscience, it is possible to model these different scales and to build the link between them [1]. In particular to describe the activity on the scale of a population of neurons by a mean-field approach, capturing some aspects of the corresponding spiking network. A recently derived mean-field model of a biophysical description of neuronal excitability shows abilities to capture synchronized activities observed in pathological states, such as seizures [2]. The system obtained is a compound of coupled differential equations which can be studied by applying timescale separation methods [3, 4]. This model is a candidate to be used within The Virtual Brain [5] for clinical applications. A detailed characterization is therefore essential. Main objectives. 1. To identify the different dynamical regimes of this model, in particular in a parameter configuration corresponding to a healthy state; 2. To determine the different timescales involved in this system; (and possibly) 3. To start a bifurcation study for identified biophysical parameters of interest. Period. Some time in 2023, in accordance with the schedule of the candidate’s courses. Location. One or both of the following addresses: Institut de Neurosciences des Systèèmes AMU Faculty of Medicine 27, Boulevard Jean Moulin 13005 Marseille, France and/or Inria centre at Université Côte d’Azur MathNeuro Project team 2004 route des Lucioles - BP 93 06902 Sophia Antipolis, France Supervisors. Damien Depannemaecker <https://www.researchgate.net/profile/Damien-Depannemaecker> (Aix-Marseille Université) and Mathieu Desroches <https://www-sop.inria.fr/members/Mathieu.Desroches/> (Inria). How to apply. Interested candidates should send a CV and a short motivation letter expressing their interest and skills for this project to: mathieu.desroches(a)inria.fr <mailto:mathieu.desroches@inria.fr> and damien.depannemaecker(a)univ-amu.fr<mailto:damien.depannemaecker@univ-amu.fr>. Selected candidates will be invited to an interview, which may take place online. For candidates requiring a visa for the EU, a period of at least three months is necessary to obtain the documents. Candidate profile. The candidate from an MSc (M2) or an engineering school must have an interest and skills in dynamical systems as well as for neuroscience. Having at least basic programming knowledge (e.g. python or matlab) is necessary for this internship. The involvement and motivation of the candidate, as well as the ability to be organized and proactive, are essential criteria in the selection of the candidate. There could be perspectives of following up with a PhD. References 1. Depannemaecker D, Destexhe A, Jirsa V, Bernard C. Modeling seizures: From single neurons to networks. Seizure. 2021 Aug;90:4–8. Available from: http://dx.doi.org/10.1016/j.seizure.2021.06.015. 2. Bandyopadhyay A, Rabuffo G, Calabrese C, Gudibanda K, Depannemaecker D, Ivanov A, et al. Mean- field approximation of network of biophysical neurons driven by conductance-based ion exchange. bioRxiv. 2022. Available from: https://www.biorxiv.org/content/early/2022/12/03/2021.10.29.466427. 3. Desroches M, Rinzel J, Rodrigues S. Classification of bursting patterns: A tale of two ducks. PLoS Com- putational Biology. 2022;18(2):e1009752. Available from: https://journals.plos.org/ploscompbiol/ article?id=10.1371/journal.pcbi.1009752. 4. Saggio ML, Spiegler A, Bernard C, Jirsa VK. Fast–Slow Bursters in the Unfolding of a High Codimension Singularity and the Ultra-slow Transitions of Classes. The Journal of Mathematical Neuroscience. 2017 Jul;7(1). Available from: http://dx.doi.org/10.1186/s13408-017-0050-8. 5. The Virtual Brain;. Available from: https://www.thevirtualbrain.org/.

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Women in Memory Research 2023
by Vinita Samarasinghe Dec. 22, 2022

Dec. 22, 2022

The event below is for women who are interested in pursuing a PhD in memory research in neuroscience or philosophy. Please be kind enough to pass on this message to interested students. ------------------------------------------------------------------------ Women in Memory Research 2023 Come and learn what an academic career looks likeand discover its advantages. During your week at the Ruhr University Bochum (RUB)you will participate in GEM 2023 <https://for2812.rub.de/gem2023/> where you will hear about the latest research in generative episodic memory, be given the opportunityto present your research and meet with female scientists from the field. Before and after GEM you'll be introduced to support structures, funding measures and the FOR 2812 labs <https://for2812.rub.de/projects/>. Our participating senior scientists include: Ali Boyle, London School of Economics; Pernille Hemmer, Rutgers University; Peggy St. Jacques, University of Alberta; Kristina Liefke, Ruhr University Bochum; Maria Wimber, University of Glasgow. Sounds exciting? *Who can apply:* Womenmasters students in their final year of study and recently graduated masters students who are looking into an academic career in the area of memory research/neuroscience. Applicants must have excellent grades and be able to communicate in English. Selection of participants is competitive. We only have 12 spots! *How to apply:* Send your application including a one page letter of motivation, a current CV, masters transcripts and a letter of recommendation from one of your professors. Your application should be sent, as a single PDF document, to Vinita Samarasinghe @ for2812+gem(a)rub.de <mailto:for2812@rub.de> by March 15, 2023 with the subject line "WiMR - application". If you need child care or any other support please note this in your application. Applications will be evaluated and ranked after the deadline has passed and notifications will be sent out by 31.03.2023. If you accept, you must register for GEM 2023. *What to expect from us:* We will provide bed and breakfast (double room occupancy), cover travel costs (restrictions apply) and provide some meals. The program is offered in English. *What we expect from you:* You are present for all of the program and that you present your current research in the form of a poster at GEM 2023. *Questions? * Visit our website at https://for2812.rub.de/wimr2023 for more information. Please feel free to get in touch with Vinita Samarasinghe (for2812(a)rub.de <mailto:for2812@rub.de>) if you have any questions. -- Vinita Samarasinghe M.Sc., M.A. Science Manager Arbeitsgruppe Computational Neuroscience Institut für Neuroinformatik Ruhr-Universität Bochum, NB 3/73 Postfachnummer 110 Universitätstr. 150 D-44801 Bochum Tel: +49 (0)234 32 27996 Email:samarasinghe@ini.rub.de

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Bernstein Conference 2023
by FM-bernstein.communication Dec. 22, 2022

Dec. 22, 2022

Dear colleagues, We are pleased to announce the Bernstein Conference 2023, which will be again in Berlin. Please highlight September 26-29, 2023, in your calendar. Check out our website and social media channels, where we will keep sharing new and detailed information as we progress. Season's greetings and a happy new year! Your Bernstein Coordination Site Bernstein Network Computational Neuroscience | Bernstein Coordination Site Branch Office of the Forschungszentrum Jülich at the University of Freiburg Hansastr. 9a | 79104 Freiburg, Germany web: www.bernstein-network.de<http://www.bernstein-network.de> Twitter: BernsteinNeuro LinkedIn: Bernstein Network Computational Neuroscience Mastodon: BernsteinNetwork(a)mastodon.world ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Postdoc opening in analysis of complex hippocampal oscillations (Demian Battaglia and Romain Goutagny's FunSy team, Strasbourg)
by BATTAGLIA Demian Dec. 20, 2022

Dec. 20, 2022

We are currently inviting applications for a full-time postdoc position under the joint co-mentoring of Dr. Demian Battaglia and Dr. Romain Goutagny (University of Strasbourg, France; Functional System's Dynamics team – FunSy, https://funsyteam.org<https://funsyteam.org/>). The position starts as soon as possible and can last up to two years. This job offer is funded by the French ANR "HippoComp" project, which focuses on the complexity of hippocampal oscillations and the hypothesis that such complexity can serve as computational resource. In our joint FunSy team, we perform electrophysiological recordings in hippocampus and cortex during spatial navigation and memory tasks in mice (wild type and mutant developing various neuropathologies) and have access to vast data through local and international cooperation. Furthermore, we use a large spectrum of computational tools ranging from time-series and network analyses, information theory and machine-learning to multi-scale computational modeling. A good idea about some of the approaches used in the lab can be found in this recent preprint: Douchamps et al. 2022. Hippocampal gamma oscillations form complex ensembles modulated by behavior and learning, bioRxiv (https://doi.org/10.1101/2022.10.17.512498) We are seeking for various profiles of candidates, with main expertise in either computational or experimental neuroscience. Computational project components would deal with numerically-intensive data analyses (dimensional reduction, encoding/decoding, design of discriminative features...). Experimental project components would focus primarily on simultaneous fiber photometry and local-fields potentials recordings, together with the pre-processing of these data. Interested candidates could have hybrid experimental/computational projects. The ideal candidate will have a doctorate in systems or computational neuroscience, with previous experience in the analysis of rich datasets. In addition, we expect programming skills (e.g., Python, C/C++, Matlab), good communication skills in English (oral and written), the ability to work well in an international team, curiosity and open-mindedness. Strasbourg University is home of an emergent and active community in neuroscience, from molecules and cells to whole brain imaging and behavior, in relation with clinics. The proximity with Germany and Switzerland is an asset allowing interactions with transnational Computational and Neuroscience teams. Strasbourg, home of important European institutions, is a small fascinating city with a rich student and cultural life, well connected via high-speed train to important European cities (e.g. less than two hours from Paris). DEADLINE FOR APPLICATION: January 15th 2023 Please send your application, including CV, motivation letter and representative publications (preprints accepted) electronically, to both PIs (Romain Goutagny and Demian Battaglia). In addition, contacts of at least two academic references must be communicated (contact email or recommendation letter attachments). Pre-selected candidates will be interviewed over Zoom or invited to give a talk if possible. We are committed to equal opportunity hiring. We strongly encourage applications from qualified women or candidates from any country. Contact persons: Demian Battaglia, dbattaglia AT unistra.fr<mailto:dbattaglia@unistra.fr> Romain Goutagny, goutagny AT unistra.fr<mailto:goutagny@unistra.fr>

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New Book: Introducing Computation to Neuroscience – Selected Papers of George Gerstein
by Dr. David Goyer Dec. 20, 2022

Dec. 20, 2022

Prof. Sonja Grün (INM-6, INM-10 & IAS-6; Jülich Research Center), together with colleagues Profs. A. Aertsen, P.E. Maldonado and G. Palm, recently published the book “Introducing Computation to Neuroscience – Selected Papers of George Gerstein <https://link.springer.com/book/10.1007/978-3-030-87447-6>”. George Gersteinhad his roots in physics and was known for his long-term commitmentto transformingneuroscience intoa field ofmore rigorous science, like physics was at the time. With this, hewas miles ahead of the ﬁeld, consistently striving for quantitative analyses, mechanistic models, and conceptual clarity. Eventually, he pioneeredwhat we now know asComputational Neuroscience-many years before the term was coined. But the overarching goal of George Gerstein’s research was always to understand the functional organization of neuronal networks in the brain. Prof. Grün and the editors nowhave compiled a selection of George Gerstein’s many seminalexperimental, theoretical andcomputational contributions to neuroscience into a single, comprehensive volume. They also provide a fresh view on the subjects of his work, as several of George Gerstein’s former students and collaborators kindly contributed introductionsto various chapters.This does not onlyframethe papers in their historical and present context, it alsoaddsthepersonal touch of their involvement in generating the papersand gives a glimpse into lab life. The book itselfis organized intoa series of chapters with differentsubjects, each one containing reprintsof George Gerstein’s papersin chronological order. Thereby, each of these chapters traces the developmentof George Gerstein’s seminal contributions to the Neurosciences, be it in the domain of neuron and network modeling or in the area of neuronal data analysis techniques. In the words of the editors: "/We hope that, taken together, these various Chapters and their Introductions will help the reader appreciate how much our current thinking on brain function owes to George Gerstein’s research and the insights gained from it. George was not only an innovative thinker in theory, experiment and analysis methodology, he also inspired by his mode of thinking science. Thus, in a way, this book is both a product of this inspiration and a tribute to it./" -- Dr. David Goyer 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 phone: +49-1756402993

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