- Comp-neuro - lists.cnsorg.org

Re: [Comp-neuro] New computational neuroscience paper on human postural control system in PLoS Comput Biol.

by André Fabio Kohn

Mesoscale neural model of human spinal cord, muscle receptors, muscle dynamics and standing control biomechanics. This recently published paper starts from neuronal ionic channels to model spinal cord neurons and ends at studying human postural control during quiet stance. It represents a closed loop system, with feedback achieved through appropriate muscle spindle and Golgi tendon organ models. It is a mesoscale model and it was successfully validated both at the individual level and the overall behavior level. Spinal cord neurons (motoneurons and excitatory and inhibitory interneurons) are modeled based on ionic channel dynamics, synapses have dynamic properties, afferent and efferent axons introduce delays, muscles and tendons are modeled based on human data, appropriate models of muscle spindles and Golgi tendon organs provide sensory feedback to the spinal cord. Brain commands on the spinal cord are modeled through Gamma point processes with appropriate parameters. >From an overall theoretical view, the system is composed of nonlinear elements, it is stochastic and has delays and is described by approximately 5000 differential equations. Among its many new results, one is that a mixture of intermittent and continuous motor control may arise from the overall dynamics of the closed loop system, without influence from the brain. Elias, L.A., Watanabe, R.N. Kohn, A.F., 2014 (November). Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10039… Andre Fabio Kohn, Ph.D. Professor of Biomedical Engineering and Neuroscience University of Sao Paulo, Brazil www.leb.usp.br 2015-01-30 18:36 GMT-02:00 André Fabio Kohn <andfkohn(a)gmail.com>: > This recently published paper starts from neuronal ionic channels to model > spinal cord neurons and ends at studying human postural control during > quiet stance. It represents a closed loop system, with feedback achieved > through appropriate muscle spindle and Golgi tendon organ models. It is a > mesoscale model and it was successfully validated both at the individual > level and the overall behavior level. Spinal cord neurons (motoneurons and > excitatory and inhibitory interneurons) are modeled based on ionic channel > dynamics, synapses have dynamic properties, afferent and efferent axons > introduce delays, muscles and tendons are modeled based on human data, > appropriate models of muscle spindles and Golgi tendon organs provide > sensory feedback to the spinal cord. Brain commands on the spinal cord are > modeled through Gamma point processes with appropriate parameters. > > From an overall theoretical view, the system is composed of nonlinear > elements, it is stochastic and has delays and is described by approximately > 5000 differential equations. > > Among its many new results, one is that a mixture of intermittent and > continuous motor control may arise from the overall dynamics of the closed > loop system, without influence from the brain. > > > > Elias, L.A., Watanabe, R.N. Kohn, A.F., 2014 (November). Spinal Mechanisms > May Provide a Combination of Intermittent and Continuous Control of Human > Posture: Predictions from a Biologically Based Neuromusculoskeletal Model > > > http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.10039… > > > > Andre Fabio Kohn, Ph.D. > > Professor of Biomedical Engineering and Neuroscience > > University of Sao Paulo, Brazil > > www.leb.usp.br >

Feb. 12, 2015

Reminder - Feb. 15 Application Deadline for 2015 Summer School on Large-Scale Brain Modelling

by Peter Blouw

[All details about this school can be found online at http://www.nengo.ca/summerschool] The Centre for Theoretical Neuroscience at the University of Waterloo is inviting applications for our 2nd annual summer school on large-scale brain modelling. This two-week school will teach participants how to use the Nengo simulation package to build state-of-the-art cognitive and neural models. Nengo has been used to build what is currently the world's largest functional brain model, Spaun <http://www.nengo.ca/build-a-brain/spaunvideos> [1], and provides users with a versatile and powerful environment for simulating cognitive and neural systems. We welcome applications from all interested graduate students, research associates, postdocs, professors, and industry professionals. No specific training in the use of modelling software is required, but we encourage applications from active researchers with a relevant background in psychology, neuroscience, cognitive science, engineering, computer science, or a related field. For a look at last year's summer school, please see this short video: http://goo.gl/BXJ3x5 [1] Eliasmith, C., Stewart T. C., Choo X., Bekolay T., DeWolf T., Tang Y., Rasmussen, D. (2012). A large-scale model of the functioning brain. Science. Vol. 338 no. 6111 pp. 1202-1205. DOI: 10.1126/science.1225266. [ http://nengo.ca/publications/spaunsciencepaper] ***Application Deadline: February 15, 2015*** Format Participants are encouraged to bring their own ideas for projects, which may focus on testing hypotheses, modelling neural or cognitive data, implementing specific behavioural functions with neurons, expanding past models, or provide a proof-of-concept of various neural mechanisms. More generally, participants will have the opportunity to: - build perceptual, motor, and cognitive models with spiking neurons - model anatomical, electrophysiological, cognitive, and behavioural data - use a variety of single cell models within a large-scale model - integrate machine learning methods into biologically oriented models - use Nengo with your favorite simulator, e.g. Brian, NEST, Neuron, etc. - interface Nengo with various kinds of neuromorphic hardware - interface Nengo with cameras and robotic systems - implement modern nonlinear control methods in neural models - and much more… Hands-on tutorials, work on individual or group projects, and talks from invited faculty members will make up the bulk of day-to-day activities. There will be a weekend break on June 13-14, and fun activities scheduled for evenings throughout. A project demonstration event will be held on the last day of the school, with prizes for strong projects! Date and Location: June 7th to June 19th, 2015 at the University of Waterloo, Ontario, Canada. Applications: Please visit http://www.nengo.ca/summerschool, where you can find more information regarding costs, travel, lodging, along with an application form listing required materials. If you have any questions about the school or the application process, please contact Peter Blouw (pblouw(a)uwaterloo.ca)

Feb. 12, 2015

Announcing Allen/UW Summer Workshop on the Dynamic Brain 2015

by Adrienne Fairhall

Applications are now open for the second Allen Institute for Brain Science/UW Summer Workshop on the Dynamic Brain. Directed by Christof Koch and Adrienne Fairhall, this course takes place on beautiful San Juan Island, WA, from Aug 23-Sept 6. The course features lectures in basics of experimental and theoretical neurobiology along with practical sessions on coding, big data, modeling and the use of the Allen Institute tools for neuroanatomical exploration and model development. Students will also have access to new high-throughput data sets collected by the Institute in the past year with which to carry out an independent project. Deadline April 1. For details and link to application, see one of: http://alleninstitute.org/summerworkshop http://courses.washington.edu/braindyn/

Feb. 12, 2015

New Book: Information Theory

by Jim Stone

I'd like to announce the publication of this book: Information Theory: A Tutorial Introduction by JV Stone Reviews, synopsis, and table of contents can be found here: http://jim-stone.staff.shef.ac.uk/BookInfoTheory/InfoTheoryBookMain.html Note that the examples explored in the final chapter are especially relevant to computational neuroscience and biology. regards, Dr Jim Stone University of Sheffield, UK. http://www.jim-stone.staff.shef.ac.uk/

Feb. 11, 2015

Postdoctoral position at Group for Neural Theory, Paris

by Srdjan Ostojic

A postdoctoral position is available in Srdjan Ostojic’s team at the Group Neural Theory, Paris, France (see http://iec-lnc.ens.fr/group-for-neural-theory/) to investigate dynamics and computations in spiking neural networks, combining theoretical approaches, simulations and analysis of neurophysiological datasets. The Group for Neural Theory is a highly interactive and dynamic environment situated in central Paris, and embedded within the strong Parisian theoretical neuroscience community. The ideal candidate should have a strong quantitative background, e.g. in computational neuroscience, physics, applied maths, computer science. Previous experience in neuroscience is preferred but not required. Starting dates are flexible. The position is for two years, with a possible extension for a third year. Candidates should send a letter of motivation (2 pages max), the contact information of 2 to 3 referees and their CVs to srdjan.ostojic at ens.fr *BEFORE March 20th, 2015*. I will be available at Cosyne for informal inquiries. Srdjan Ostojic Group for Neural Theory Ecole Normale Superieure Paris 29, rue d'Ulm 75005 Paris, France

Feb. 11, 2015

Open PhD position in MEG/EEG research at Research Center Juelich, Germany

by Martina Reske

We have an open PhD student position in our collaborative project entitled “From spike trains to whole-brain dynamics – Bottom-up and top-down processing during active vision” to fill. This project addresses the question how visual input is processed in extremely short time cycles of fixations and saccades through interaction of various cortical areas. MEG recordings from human subjects performing free viewing tasks will allow for the simultaneous observation of neuronal activities from different cortical areas during active vision. Analysis of subjects’ performance and brain activity on these visual tasks enables us to study the information flow through various cortical areas, and to identify top-down components interacting with bottom-up processes. What we expect from you: * We seek for a highly motivated candidate with curiosity and persistence * A preferable candidate will have background and strong Master degree in physics, neuroscience, electrophysiology, biology, computer science or a closely related field of natural science, preferably in the field of MEG/EEG biophysics, data acquisition and analysis, biostatistics, MEG/EEG biophysics or signal processing * Obligatory: excellent educational records in the related field, good programming and data processing skills, time series analysis and M/EEG source estimation * Substantial expertise in scientific programming (preferable languages: Python, C, C++ ) and substantial knowledge of Linux and Windows * Strong motivation to carry out neuroimaging studies utilizing MEG and to perform source and connectivity analysis * Beneficial: basic knowledge of neuroscience concepts * Ability and willingness to work independently and proactively * Confident appearance and ability to work cooperatively in an interdisciplinary environment * Good interpersonal and communication skills, structured and systematic working style * Fluent in English (spoken and written); beneficial: knowledge of German The candidate will primarily be based at the Jülich Research Center. What we offer: We offer a position in a creative and international team, themes ranging from computational neuroscience, simulation technology and multimodal imaging, see www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> and http://www.fz-juelich.de/inm/inm-4/EN/Forschung/MEG-Physik/_node.html. 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. Applications, including a letter clearly motivating your application, 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 CSC-GID latest until March 31st , 2015, to should be sent to: Dr. Martina Reske (m.reske(a)fz-juelich.de<mailto:m.reske@fz-juelich.de>) – Scientific Coordinator. Project leaders will be: Prof. Dr. Sonja Grün (INM-6/IAS-6), Dr. Junji Ito (INM-6/IAS-6), Dr. Jürgen Dammers (INM-4) Institute of Neuroscience and Medicine (INM-6, INM-4), Institute for Advanced Simulation (IAS-6), Jülich Research Center and JARA52425 Jülich, Germany, www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> -- 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Feb. 11, 2015

Ikerbasque Research Fellow ("Tenure"). Methods in Neuroimaging, Bilbao (Spain)

by Jesus Cortes

Dear researcher, One position for "Ikerbasque Research Fellow" will be host by the new emerging group of Computational Neuroimaging in Biocruces. http://www.biocruces.com/web/biocruces/bc5.08 More information about the position, "Ikerbasque Research Fellow" at http://www.ikerbasque.net/fellows More information about Biocruces http://www.biocruces.com/ Interested researchers must contact me before April 1, 2015. Feel free in contacting me for any further question or comment. Provide a copy of an updated CV remarking best 5 publications. Prof. Jesus M Cortes Ikerbasque Research Professor Head of the Computational Neuroimaging Lab Biocruces Health Research Institute

Feb. 11, 2015

Introductory Workshop on Computational Methods in Neuroscience, June 10 – 19, 2015

by Artur Luczak

Campus Alberta Neuroscience is pleased to announce the second annual Introductory Workshop on Computational Methods in Neuroscience. This ten-day workshop is comprised of lectures and hands-on Matlab exercises to introduce students to neuronal data analysis methods. Workshop is aimed for graduate students with little priory experience in quantitative methods who wants to learn Matlab and its application for data analyses. Most costs – including registration fees, travel to Lethbridge, accommodation, and most meals – will be covered for Alberta trainees. Individuals from outside of Alberta are encouraged to apply, but must cover their own costs. These costs are estimated to be around $1300 (excluding travel). Registration for the workshop is now open – complete applications must be received by March 10, 2015 at albertaneuro(a)uleth.ca . Workshop will take place at University of Lethbridge, Alberta, Canada, June 10 – 19, 2015. Course Director is Dr. Bruce McNaughton and course instructors include Drs David Euston, Aaron Gruber, Artur Luczak, Masami Tatsuno and Majid Mohajerani. Further information and application details are available at: www.albertaneuro.ca/workshop Cheers, Artur ------------------------------------------------ Artur Luczak, Ph.D., Assoc. Professor Canadian Centre for Behavioural Neuroscience Department of Neuroscience, University of Lethbridge 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada tel.: (403) 394-3974; fax: (403) 329-2775 http://lethbridgebraindynamics.com/artur_luczak

Feb. 10, 2015

Berkeley course in mining and modeling neuroscience data, July 6-17, 2015

by Jeff Teeters

Call for applications: We invite applicants to the 2015 summer course in "Mining and modeling of neuroscience data" to be held July 6-17 at UC Berkeley. A description of the course is below and also at: http://crcns.org/course Application deadline is April 6 (or March 1, for MSRI's sponsored students). ----- Berkeley summer course in mining and modeling of neuroscience data July 6-17, 2015 Redwood Center for Theoretical Neuroscience, UC Berkeley Organizers: Fritz Sommer, Bruno Olshausen, Jeff Teeters (HWNI, UC Berkeley); Christos Papadimitriou (Simons Institute, Berkeley); Ingrid Daubechies (MSRI, Duke). Scope This course is for students and researchers with backgrounds in mathematics and computational sciences who are interested in applying their skills toward problems in neuroscience. It will introduce the major open questions of neuroscience and teach state-of–the-art techniques for analyzing and modeling neuroscience data sets. The course is designed for students at the graduate level and researchers with background in a quantitative field such as engineering, mathematics, physics or computer science who may or may not have a specific neuroscience background. The goal of this summer course is to help researchers find new exciting research areas and at the same time to strengthen quantitative expertise in the field of neuroscience. The course is sponsored by the National Science Foundation from a grant supporting activities at the data sharing repository CRCNS.org, the Helen Wills Neuroscience Institute, the Simons Institute for the Theory of Computing and the Mathematical Science Research Institute. Format The course is “hands on” in that it will include exercises in how to use and modify existing software tools and apply them to data sets, such as those available in the CRCNS.org repository. Course Instructors Vitaly Feldman, IBM Almaden Research Center Sonja Grün, Juelich Research Center, Germany Robert Kass, Carnegie Mellon University, Pittsburgh Maneesh Sahani, Gatsby Unit, University College London Odelia Schwartz, University of Miami Eric Shea-Brown, University of Washington Frederic Theunissen, UC Berkeley Course Moderators Fritz Sommer and Jeff Teeters, Redwood Center for Theoretical Neuroscience Speakers To complement the main course instruction there will be lectures in the evenings by local Berkeley and UCSF neuroscientists presenting their research using quantitative approaches. Requirements Applicants should be familiar with linear algebra, probability, differential and integral calculus and have some experience using MatLab and Python. Each student should bring a laptop with the software installed. Cost There is no cost to attend. Assistance for travel, housing and food costs is in general not provided, (except for students who are sponsored by MSRI or the Simons Institute; see below). Potential financial support Support for a limited number of students to attend will be provided through both MSRI and the Simons Institute for the Theory of computing. Applicants who are at a MSRI partner institution can be admitted to the course and receive support for attending through MSRI as described at: http://www.msri.org/web/msri/scientific/workshops/summer-graduate-school Applicants with a Computer Science background are invited to apply for support by the Simons Institute for the Theory of Computing and the Computer Community Consortium (CCC). See “How to Apply” section. Housing There may be some limited dorm housing available. Cost is $742 per person in a shared double room, which includes an all-you-can-eat buffet dinner on evenings that meals are not supplied with the course. We will help coordinate sharing of dorm rooms for those who wish to stay in the dorms. Other housing options include: a hostel near campus ( http://berkeleyhostel.com) which is $32 / night for a bed in shared dorm room; nearby hotels (http://visitberkeley.com/stay) and accommodations advertised through craigslist.org and airbnb.org. We will help students setup groups to search for shared housing together. Food Most meals are not included with the course, although breakfast items, snacks and some dinners will be provided. Food for other meals can be purchased at the dorm cafeteria and local restaurants. How to apply There are two methods of applying. Method 1) Students at a MSRI partner institution can be admitted to the course and receive support for attending through MSRI as described at: http://www.msri.org/web/msri/scientific/workshops/summer-graduate-school Method 2) All non-MSRI applications are submitted via the online form linked from: http://crcns.org/course. A curriculum vitae and a letter of recommendation are required. Those applying using method 1 can also apply using method 2 (in case the MSRI supported positions are all taken). Applicants with a computer science background who wish to apply for support from the Simons Institute for the Theory of Computing must apply using method 2 and include additional information as instructed on the application form. The course is limited to 25 students. Deadlines Applications must be received by April 6 (or March 1, for MSRI’s sponsored students). Notifications of acceptance will be given by the end of April. If staying in dorm housing, and not sponsored by MSRI or the Simons Institute, payment for housing and the meal plan must be received one week before the start of the course. Questions Questions about the course can be sent to course [at] crcns.org. Topics covered Basic approaches: - The problem of neural coding - Spike trains, point processes, and firing rate - Statistical thinking in neuroscience - Theory of model fitting / regularization / hypothesis testing - Bayesian methods - Spike sorting - Estimation of stimulus-response functionals: regression methods, spike-triggered covariance - Variance analysis of neural response - Estimation of SNR. Coherence Information theoretic approaches: - Information transmission rates and maximally informative dimensions - Scene statistics approaches and neural modeling Techniques for analyzing multiple-unit recordings: - Cross-correlation and JPSTH - Sparse coding/ICA methods, vanilla and methods including statistical models of nonlinear dependencies - Unitary event analysis - Methods for detection of higher-order correlations - Correlation approaches for massively parallel spike trains - Proper surrogates for spike synchrony analysis - Methods for assessing functional connectivity - Advanced topics in generalized linear models - Low-dimensional latent dynamical structure in network activity–Gaussian process factor analysis/newer methods Towards building a theory of the brain: - Applications of mathematical analysis of dynamical systems in neuroscience - Approaches based on methods from theoretical computer science

Feb. 10, 2015

Final program, qbio seminar in Bilbao, February 17-18, 2015

by Jesus Cortes

This is the final program for the BCAM workshop in Quantitative Biomedicine next week Tuesday, February 17, 2015 9:30-11:30. Session 1. 09:30-10:10 Joanna Tyrcha. Stochastic stability and dynamic behavior of a compound cell-cycle model 10:10-10:50 Mathieu Desroches. Mixed-Mode Bursting Oscillations (MMBOs): slow passage through spike-adding canard explosion 10:50-11:30 Albert Granados. The period adding phenomenon in periodically driven hybrid spiking models 11:30-12:10. Coffee Break 12:10-14:10 Session 2. 12:10-12:50 Edward J. Vigmond. Cardiac Applications of Computational Electrophysiology 12:50-13:30 Pablo Lamata. Extraction of diastolic biomarkers through personalization of computational models 13:30-14:10 Aciel Eshky. Condition Monitoring of Athletes with a Wearable Heart Rate Variability Sensor 14:10-15:20 Lunch 15:20-18:00. Session 3. 15:20-16:00 Cesar Caballero. The power of haemodynamic deconvolution for mapping brain dynamics with BOLD functional MRI 16:00-16:40 Andrea Fuster. Geometric framework for diffusion MR images of the brain: theory and applications 16:40-17:20 Ernesto Sanz-Arigita. Multimodality MRI in different groups at risk for developing Alzheimer’s disease: towards multidimensional brain imaging biomarkers. 17:20-18:00 Pierrick Coupe. New patch-based estimators for early detection of Alzheimer’s disease Wednesday, February 18, 2015 9:30-11:30. Session 4. 09:30-10:10 Bert Kappen. Explaining missing heritability with Gaussian Process regression 10:10-10:50 Alberto Llera. Efficient Gaussian/Inverse Gammas mixture-models: a new tool for thresholding ICA statistical maps from fMRI data 10:50-11:30 Estibaliz Garrote. Computer vision applied to digital pathology: image search engine based on clinical similarity 11:30-12:10 Coffee Break 12:10-14:10. Session 5. 12:10-12:50 Michael Wibral. Information transfer and causal interactions - Conceptual differences and combined analyses strategies 12:50-13:30 Luca Faes. Dynamics of Information Storage, Transfer and Modification in the Cardiovascular System 13:30-14:10 Adam Barrett. Synergistic and redundant information sharing in Gaussian systems 14:10-15:20 Lunch 15:20-18:00. Session 6. 15:20-16:00 Ruedi Stoop. Power-law size distribution of activated avalanches - what do they really mean? 16:00-16:40 Daniele Marinazzo. Tracking slow modulations in synaptic gain using dynamic causal modelling: Validation in epilepsy 16:40-17:20 Paolo Paradisi. Intermittency-based complexity measures in brain EEG data 17:20-18:00 Jordi Soriano. Experiments in Neuronal Cultures: Exploring Open Questions in Physics and Medicine

Feb. 10, 2015