August 2018 - Comp-neuro - lists.cnsorg.org

The Journal of Mathematical Neuroscience - recent articles

by Stephen Coombes

The Journal of Mathematical Neuroscience publishes research articles on the mathematical modelling and analysis of all areas of neuroscience. The new Impact Factor of the journal is 2.414 The current list of journal articles is available at http://www.mathematical-neuroscience.com/ : Stochastic Hybrid Systems in Cellular Neuroscience Paul C. Bressloff and James N. Maclaurin https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Data Assimilation Methods for Neuronal State and Parameter Estimation Matthew J. Moye and Casey O. Diekman https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Bifurcations of Limit Cycles in a Reduced Model of the Xenopus Tadpole Central Pattern Generator Andrea Ferrario, Robert Merrison-Hort, Stephen R. Soffe, Wen-Chang Li and Roman Borisyuk https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… What Is Required for Neuronal Calcium Waves? A Numerical Parameter Study Markus Breit and Gillian Queisser https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Investigating the Correlation–Firing Rate Relationship in Heterogeneous Recurrent Networks Andrea K. Barreiro and Cheng Ly https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… All articles are Open Access. ------------------------------------------------------- Stephen Coombes Professor of Applied Mathematics School of Mathematical Sciences Nottingham, UK Tel: 0115 846 7836 http://www.maths.nott.ac.uk/~sc/ ------------------------------------------------------- This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

Aug. 28, 2018

Frontiers Research Topic on Data Assimilation

by Axel Hutt

Announcement of the Frontiers Research Topic -------------------------------------------------------------------------------------- Data Assimilation of Nonlocal Observations in Complex Systems -------------------------------------------------------------------------------------- Natural complex systems exhibit spatio-temporal dynamics on multiple scales that are difficult to predict and understand. To gain deeper insights into the system's dynamics and to be able to predict its evolution, observations of that system are analyzed which allows to derive or motivate models that fit that system. In general, one may distinguish two types of data. The so-called in-situ or local observations capture direct measurements of the system itself, such as temperature at a specific height in the atmosphere or electric potentials in biological cells. Other observations are not measured at a certain location but represent the integral of some relevant quantities manifesting the system's activity. Examples in meteorology for such nonlocal observations are satellite radiances, slant delays and radio occultation based on GPS data, or radar reflectivities. In biological systems, the non-invasive measurement techniques provide nonlocal observations, such as electro- and magnetoencephalogram or Magnetic Resonance Imaging. In addition to observations, realistic models are essential to improve the understanding of natural complex systems and to predict their dynamical evolution. To merge both models and observations, it is essential to develop techniques that optimally estimate the system activity well-adapted to a model and observed data. Data assimilation comprises a number of methods to merge diverse experimental data with an underlying model. Data assimilation optimally combines observations and a model to achieve a certain goal, such as optimal fitting of model parameters or providing optimal forecasts of the system's dynamics. Since the recent years have shown an increasing number of observation techniques capturing integrals of system activity, data assimilation of nonlocal observations becomes more and more important. The present Research Topic aims to bring together recent theoretical work in data assimilation of nonlocal observations with a strong link to specific applications. This article collection reflects the state-of-the-art in this research field. Examples of theoretical topics (as an unconstrained open list) are Kalman filters, variational assimilation techniques, regression techniques and stochastic optimization techniques. Applications may range from the parameter estimation in genetic regulatory networks over prediction of brain dynamics to weather forecast. We invite you to submit an abstract until November 30, 2018 and the manuscript until June 30, 2019. Contributions will be published as soon as they are accepted and synchronously gathered in the Research Topic volume. For more information, do not hesitate to contact us (email of Axel Hutt: digitalesbad(a)gmail.com) The organisers Lili Lei (Nanjing University) Marc Bocquet (Ecole des Ponts ParisTech) Alberto Carrassi (Nansen Environmental Remote Sensing Center) Axel Hutt (Deutscher Wetterdienst) Roland Potthast (Deutscher Wetterdienst) -- Axel Hutt Directeur de Recherche Deutscher Wetterdienst - German Meteorological Service Research and Development, Department FE 12 (Data Assimilation) Frankfurter Strasse 135, 63067 Offenbach, Germany Tel.: +49 69 8062 2750 http://www.geocities.ws/digitalbath/

Aug. 27, 2018

LACONEU Summer School - January 2019

by Patricio Orio

----------------------------------------------------------------------- We have the pleasure to invite Graduate and Undergraduate students to participate in: ----------------------------------------------------------------------- LACONEU 2019 V Latin American Summer School in Computational Neuroscience Special Topic: Complex Systems and Network Connectivity January 7-25th, 2019 Valparaíso - CHILE http://www.laconeu.cl ----------------------------------------------------------------------- The principal aims of LACONEU 2019 Summer School are to disseminate and to develop Computational Neuroscience in Latin America, gathering researchers and students with common interests in the beautiful and historical city of Valparaiso, in Chile. LACONEU 2019 expects to foster a collaborative exchange between the attendees, researchers and students, based on fundamental theoretical and practical knowledge, and thus, to help the establishment of strong, long-term collaborations. This version also includes a WORKSHOP on January 16th, 2019 CONFIRMED SPEAKERS: - Demian Battaglia, Theoretical Neuroscience Group, INT, France - Joana Cabral, University of Oxford, UK - Bruno Cessac, INRIA Sophia-Antipolis, France - Dante Chialvo, Universidad Nacional de San Martín, Argentina - Rodrigo Cofré, Universidad de Valparaíso, Chile - Mauro Copelli, Federal University of Pernambuco, Brazil - Maxime Descoteaux, Université de Sherbrook, Canada - Wael El-Deredy, Universidad de Valparaíso, Chile - Pamela Guevara, Universidad de Concepción, Chile - María-José Escobar, Universidad Técnica Federico Santa María, Valparaíso, Chile - Henrik Jensen, Imperial College London, UK - Thierry Mora, École Normale Superiéure, France - Patricio Orio, Universidad de Valparaíso, Chile - Adrián Palacios, Universidad de Valparaíso, Chile - Tomás Pérez Acle, Fundación Ciencia y Vida, Chile - Peter Robinson, The University of Sydney, Australia - Fernando Rosas, Imperial College London, UK - Inés Samengo, Centro Atómico Bariloche e Instituto Balseiro, Argentina IMPORTANT DATES - Call for Applications: June 8th, 2018 - Application submission deadline: September 15th, 2018 (visit the webpage to see the details) - Acceptance notification: October 31st, 2018 TRAVEL GRANTS ARE AVAILABLE FOR LATIN AMERICAN STUDENTS Looking forward to see you in January! *Prof. Patricio Orio* Centro Interdisciplinario de Neurociencias de Valparaíso *CINV* Facultad de Ciencias, *Universidad de Valparaíso, Chile* +56 32 299 5538 / 32 250 8040

Aug. 24, 2018

Postdoc at RIKEN Center for Brain Science, Japan

by Taro Toyoizumi

A postdoc position is available at Lab for Neural Computation and Adaptation, RIKEN Center for Brain Science, Japan http://toyoizumilab.brain.riken.jp/ to work with Taro Toyoizumi. Job: https://cbs.riken.jp/en/careers/20180817_w929_t_toyoizumi_r.html Our lab is interested in modeling activity-dependent synaptic plasticity and dynamic information processing by the neurons in the brain. We seek highly motivated postdoctoral researchers with a strong analytical background and interest in neuroscience. Applicants should have a PhD in physics, neuroscience, mathematics, computer science, engineering, or a related area. Applicants should email a CV and a list of publications to toyoizumilab(a)ml.riken.jp In addition, applicants should organize two letters of recommendation, to be sent by the referees to toyoizumilab(a)ml.riken.jp

Aug. 23, 2018

NEST 2.16.0 released

by Hans Ekkehard Plesser

Dear colleagues! I am very excited to inform you that we have released version 2.16.0 of NEST, the Neural Simulation Tool, today. NEST 2.16.0 is the result of 89 merged pull requests by 39 developers since we released NEST 2.14.0 in October 2017. Most notably, this release includes a new infrastructure for the storage of connections, which reduces the memory consumption and network build times (Jordan et al., 2018) and extends the rate model framework for novel use-cases (Senden et al., 2018). As usual, it also includes numerous bug fixes and minor improvements. At the same time, the we have tried to minimize changes to the user interface, so scripts that worked with NEST 2.14.0 should work with NEST 2.16.0 as well. One exception is that global spike detectors have been removed, but this should be relevant only for users on petascale machines. For a detailed list of changes, please see https://github.com/nest/nest-simulator/releases/tag/v2.16.0 The citation for NEST 2.16.0 is Linssen, Charl, Lepperød, Mikkel Elle, Mitchell, Jessica, Pronold, Jari, Eppler, Jochen Martin, Keup, Chrisitan, … Plesser, Hans Ekkehard. (2018, August 27). NEST 2.16.0 (Version 2.16.0). Zenodo. http://doi.org/10.5281/zenodo.1400175 We would like to encourage you to switch to NEST 2.16.0 as soon as possible and are looking forward to hearing about your experiences! On behalf of the NEST Initiative, I would like to thank all developers who have contributed to NEST 2.16.0 and especially our release managers Dennis Terhorst and Jochen Eppler for wrapping it all up! Best regards, Hans Ekkehard Plesser President, The NEST Initiative -- Dr. Hans Ekkehard Plesser Associate Professor Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser

Aug. 21, 2018

Human Neocortical Neurosolver: A new tool for circuit level investigation of MEG/EEG data

by Stephanie Jones

We are excited to announce the first release of a new user-friendly software package for circuit level interpretation of human EEG/MEG data: Human Neocortical Neurosolver (HNN). The foundation of HNN is a computational neural model that simulates the electrical activity of the neocortical cells and circuits that generate the primary electrical currents underlying EEG/MEG recordings. HNN is a free open source package that was designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on the circuit origin of their data. We provide tutorials on how to import your data and to begin to understand the underlying neural mechanisms. The tutorials focus on some of the most commonly measured signals, including event related potentials and low frequency alpha, beta and gamma rhythms. We are eager to help users get started and have developed a user forum for feedback and questions. HNN is distributed at https://hnn.brown.edu <https://hnn.brown.edu/>. HNN is being developed by a collaborative team at Brown, MGH and Yale. HNN developments are funded by the National Institute of Biomedical Imaging and Bioengineering through the BRAIN Initiative: Theories, Models, and Methods of Analysis of Complex Data from the Brain. ******************************************* Stephanie R. Jones, PhD - on behalf of the development team Associate Professor Brown University Department of Neuroscience Stephanie_Jones(a)Brown.edu https://www.brown.edu/research/labs/jones/

Aug. 21, 2018

Full-time industry position: Computational Neuroscience / Neuromorphic Machine Learning

by Dylan Muir

aiCTX is an ultra-low-power neuromorphic computing startup / spin-off of the Institute of Neuroinformatics of the University of Zurich and the ETH Zurich. aiCTX has an immediate opening for a Neuromorphic Machine Learning R&D Engineer We are looking particularly for comp. neurosci. researchers, with a background in theory and/or modelling of spiking neural networks. This position is for a full-time on-going contract, in Zürich Switzerland. We also have paid internships available for qualified candidates. Please see the job posting for more details, and to apply: http://bit.ly/aiCTX_job2 <http://bit.ly/aiCTX_job2>

Aug. 17, 2018

Funded mathematics PhD position - Designing the dynamics of coupled oscillators - University of Exeter

by Purcell, Sarah

Funded mathematics PhD position - Designing the dynamics of coupled oscillators University of Exeter<https://www.exeter.ac.uk/>, UK Supervisors: - Dr Christian Bick<http://empslocal.ex.ac.uk/people/staff/cb618/> - Dr Kyle Wedgwood <http://emps.exeter.ac.uk/mathematics/staff/kcaw201> The University of Exeter's College of Engineering, Mathematics and Physical Sciences is inviting applications for a fully-funded PhD studentship to commence in September 2018 or as soon as possible thereafter. For eligible students the studentship will cover tuition fees in full plus an annual tax-free stipend of at least £14,777 for 3.5 years full-time, or pro rata for part-time study. The student would be based in the Department of Mathematics in the College of Engineering, Mathematics and Physical Sciences in Exeter. Networks of interacting oscillatory units are abundant in nature and technology. Their function and dynamics governs crucial aspects of our lives, ranging from the stability of power grids to the dynamics of the human brain. The dynamics of oscillator networks depends on (1) which oscillators interact with which other oscillator and (2) how oscillators interact with one another. This project will contribute to the question how the interplay between these two factors shape the network dynamics. The main aim of this PhD project is to develop theoretical and numerical approaches how oscillator networks can be designed to have specific interactions. This will allow to generate networks that exhibit a range of synchronized and locally synchronized dynamics. Moreover, the supervisor is currently collaborating with the experimental group of Istvan Z Kiss in St Louis (USA) who are working on electrochemical oscillators. Hence, there may be an opportunity to help implement the theoretical results in real-world experimental systems. The studentship will be awarded on the basis of merit for 3.5 years of full-time study to commence in September 2018 or on a mutually agreed date as soon as possible thereafter, and is subject to confirmation of funding. For full details please see the PhD advert<https://www.exeter.ac.uk/studying/funding/award/?id=3189>. If you have any questions, please get in touch with Dr Christian Bick<http://empslocal.ex.ac.uk/people/staff/cb618/> or Dr Kyle Wedgwood. <http://emps.exeter.ac.uk/mathematics/staff/kcaw201>

Aug. 17, 2018

Postdoc available in Brinkman group at Stony Brook University

by Braden Brinkman

A postdoctoral position is available in Braden Brinkman's group in the Department of Neurobiology and Behavior at Stony Brook University, located on Long Island in New York State. The Brinkman group studies mathematical models of sensory coding and network dynamics, with a focus on how environmental and physiological constraints shape coding and computation in the brain. For more information on our work and the department, please visit https://medicine.stonybrookmedicine.edu/node/14355 Candidates must have a strong background in quantitative methods; background in statistical physics is a plus. Please submit applications through Stony Brook's jobs portal here (job # 1802370): https://stonybrooku.taleo.net/careersection/post_docs/jobdetail.ftl?job=180… Complete applications must include 1. C.V. including a list of publications/preprints, research experience, and education 2. A 1-2 page summary of previous research accomplishments 3. A 1-2 page description of future research goals and interests 4. 2-3 references letters from scientists familiar with the candidates work Items 1-3 may be attached through the online application portal. Letter writers should send letters directly to braden.brinkman(a)stonybrook.edu Deadline for applications is Sept 1. Please email braden.brinkman(a)stonybrook.edu with any questions.

Aug. 16, 2018

Contrat post-doctorant 2018-2020 - Laboratoire FrontLAB, Institut du Cerveau et de la Moelle Epinière (ICM), PARIS (FR)

by Bénédicte BATRANCOURT

*Contrat post-doctoral 2018-2020* Laboratoire FrontLAB, Institut du Cerveau et de la Moelle Epinière (ICM), PARIS Inserm, U 1127, CNRS, UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127 https://icm-institute.org/fr/ L’Institut du Cerveau et de la Moelle épinière (ICM) est un centre de recherche de dimension internationale, innovant dans sa conception comme dans son organisation. En réunissant en un même lieu malades, médecins et chercheurs, l’objectif est de permettre la mise au point rapide de traitements pour les lésions du système nerveux afin de les appliquer aux patients dans les meilleurs délais. D’un point de vue scientifique, les équipes de recherche sont indépendantes, mais alliées entre elles par des Programmes Transversaux de Recherche favorisant la mutualisation des compétences. La recherche se décline selon trois modèles : la recherche fondamentale orientée vers les domaines fondamentaux d’une discipline, la recherche clinique dans laquelle le sujet participe à des protocoles pour améliorer la connaissance d’une pathologie ou d’une thérapeutique et la recherche translationnelle qui permet aux patients de bénéficier plus rapidement des innovations diagnostiques et thérapeutiques. La recherche à l’ICM couvre 4 domaines scientifiques majeurs : Neurosciences Moléculaires et Cellulaires, Neurophysiologie intégrée, Neurosciences Cognitives, Neurosciences Cliniques et Translationnelles. Dans notre équipe FRONTlab (Richard LEVY, Bruno DUBOIS), nous travaillons sur les fonctions mentales élaborées par les lobes frontaux. L’un des enjeux majeurs des neurosciences est de connaître en profondeur les fonctions frontales afin de *comprendre comment sont élaborés et contrôlés nos comportements les plus complexes* (prise de décision, planification raisonnement, créativité, jugement moral, interactions sociales…). Une connaissance approfondie des lobes frontaux est aussi indispensable pour mieux traiter les nombreuses maladies neurologiques et psychiatriques s’accompagnant d’une atteinte des lobes frontaux (maladie d’Alzheimer, AVC, traumatismes crâniens, dépression, schizophrénie…). Nos objectifs sont de mieux cerner l’implication des lobes frontaux dans le comportement humain et les fonctions intellectuelles les plus élaborées, et de transférer les connaissances acquises vers la pratique médicale. Nous proposons un contrat de postdoctorant de 2 ans afin de participer au développement du projet ECOCAPTURE, permettant d’évaluer l’apathie de façon quantitative et objective, par l’observation du sujet en condition proche de la vie réelle. L’étude ECOCAPTURE se déroule dans la plate-forme de recherche de psychologie expérimentale de l'ICM (PRISME) qui est consacrée à l'exploration fonctionnelle du comportement humain dans des situations écologiques. L’étude ECOCAPTURE a débuté en septembre 2017, et porte sur 75 patients (Démence Fronto-Temporale, Parkinson, Dépression) et 60 volontaires sains. A ce jour 16 participants ont été inclus (8 patients et 8 volontaires sains). Dans cette étude et la phase dite de laboratoire, *l’apathie est évaluée en condition observationnelle* grâce à un système qui enregistre le comportement du sujet à l’aide d’un système à base de vidéo et de capteurs, durant une session expérimentale de 45 mn « proche de la vie réelle » qui se déroule dans une salle d’attente, selon un scénario contrôlé. L’objectif principal de l’étude ECOCAPTURE est de montrer que l’outil ECOCAPTURE basé sur des enregistrements vidéo et des capteurs d’activité et de mouvements, possède une valeur d’outil diagnostique de l’apathie. La méthode générale concerne en l’extraction de métriques comportementales à partir des données vidéo et des données extraites d’un accéléromètre 3D afin de différencier le comportement des patients de celui des sujets volontaires sains. L’étude ECOCAPTURE est la première étape d'un programme en trois phases visant à mieux évaluer l'apathie en situation « proche de la vie réelle » et à proposer de nouveaux traitements. La première phase dite « de laboratoire » a pour objectif la mise en œuvre d’un outil diagnostic de l'apathie produisant une « signature simple du comportement dirigé vers un but » ou « signature comportementale de l’apathie » permettant d'évaluer l'apathie, en situation de vie quotidienne, de façon objective (un marqueur d'apathie). Nous espérons que la création et la validation de cet outil ECOCAPTURE rendra possible dans une deuxième phase, son utilisation en clinique ainsi qu’une évaluation au domicile *ECOCAPTURE@home* avec un système de capteurs embarqués : un « holter d'apathie ». Une troisième phase visera à proposer un traitement des conséquences de l'apathie dans la vie quotidienne. L’objectif de ce contrat postdoctoral est de développer la deuxième phase : *ECOCAPTURE@home*. Nous recherchons un candidat titulaire d’un doctorat en neurosciences, sciences cognitives ou en bioinformatique, de formation : psychologue, neuropsychologue, neurologue, psychiatre, éthologue ou ingénieur biomédical. Le candidat devra posséder plusieurs compétences parmi la liste suivante : neuropsychologie, éthologie, mesure du comportement, instruments neuropsychologiques, qualités psychométriques d’un outil d’évaluation, capteurs et actigraphie, statistiques, fusion de données, classification. Une bonne connaissance de la langue française est indispensable afin de permettre les interactions avec les patients et leurs aidants. Ce contrat permettra à un chercheur motivé de participer à un projet multidisciplinaire et très original, de collaborer avec des chercheurs de disciplines diverses, de bénéficier d’un environnement scientifique international et stimulant, et de participer à la vie de l’équipe FrontLAB constituée d’un groupe de 12 PI chacun responsable d’un projet dédié à la compréhension du lobe frontal, et accueillant chaque année de nombreux étudiants. *La rémunération sera établie en fonction du barème de rémunération des contractuels Inserm* Merci d’envoyer votre CV avec une lettre de motivation et les noms et emails de deux personnes de référence à Bénédicte BATRANCOURT ( benedicte.batrancourt(a)upmc.fr) avant le 30 septembre 2018. Bénédicte Batrancourt ICM, UPMC, INSERM UMR_S 1127, CNRS UMR 7225 Hôpital Pitié-Salpêtrière 47 Boulevard de l’Hôpital F-75651 PARIS Cedex 13 Tel : 01 57 27 41 59 Tel : 06 60 44 79 79 benedicte.batrancourt(a)upmc.fr http://icm-institute.org ----------------------------------- Afin de contribuer au respect de l'environnement, merci de n'imprimer ce mail qu'en cas de nécessité.

Aug. 16, 2018