December 2017 - Comp-neuro - lists.cnsorg.org

Department of Scientific Computing

by Gordon Erlebacher

Dear Colleagues, Florida State State University’s Department of Scientific Computing (DSC; https://sc.fsu.edu) is currently accepting applications for its interdisciplinary Masters and PhD programs. These programs provide graduate students broad and deep knowledge of the fundamental techniques used in computational modeling and data science, significant exposure to at least one application domain, and the opportunity to conduct significant original research in algorithms and/or applications relating to computational and data science,including deep learning and neuroscience. A brief overview of the MS and PhD programs can be found at http://sc.fsu.edu/education . To be considered for funding, the deadline for application for the Fall 2018 cohort is January 15, 2018. Application information can be found at https://www.sc.fsu.edu/graduate/application. Self-funded applicants interested in our one-year MS program are considered throughout the Spring Semester. Please forward this message (and the attached brochure) along to any students that you think might be interested in our graduate program. Requests for more information and questions about the graduate programs or about the Department of Scientific Computing should be addressed to the Graduate Coordinator Dr. Sachin Shanbhag at sshanbhag(a)fsu.edu or to the Chair Gordon Erlebacher (Chair) at gerlebacher(a)fsu.edu. Thank you! Regards, Gordon /Erlebacher ------------- Gordon Erlebacher Chair, Department of Scientific Computing Florida State University https://sc.fsu.edu -- Gordon Erlebacher Chair, Department of Scientific Computing

Dec. 31, 2017

BioSystems - Special Issue on Neural Coding 2016 (Vol. 161, November 2017)

by Lubomir Kostal

Dear Colleagues, We would like to announce a BioSystems Special Issue on Neural Coding: BioSystems -- Volume 161 - November 2017 Available online for download now from: https://www.sciencedirect.com/science/journal/03032647/161/supp/C?sdc=1 The Table of Contents of this special issue can be seen at the end of this email. Best wishes for a happy new year, Guest Editors Chris Christodoulou, Lubomir Kostal and Angar Büschges ------------------------------------------------------------------------------------------ ------------------ BioSystems - Contents -- Volume 161 - November 2017 Special Issue: Neural Coding 2016 (Selected papers presented at the Twelventh International Workshop on Neural Coding, Cologne, Germany, 2016) Available online for download now from: https://www.sciencedirect.com/science/journal/03032647/161/supp/C?sdc=1 Editorial Chris Christodoulou, Lubomir Kostal and Angar Büschges To swim or not to swim: A population-level model of Xenopus tadpole decision making and locomotor behaviour Roman Borisyuk, Robert Merrison-Hort, Steve R. Soffe, Stella Koutsikou, Wen-Chang Li Linked Gauss-Diffusion processes for modeling a finite-size neuronal network M. F. Carfora, E. Pirozzi Information reduction in a reverberatory neuronal network through convergence to complex oscillatory firing patterns A. Vidybida, O. Shchur Efficiency of rate and latency coding with respect to metabolic cost and time Marie Levakova A single spike deteriorates synaptic conductance estimation Ryota Kobayashi, Hiroshi Nishimaru, Hisao Nishijo, Petr Lansky Synchrony measure for a neuron driven by excitatory and inhibitory inputs and its adaptation to experimentally-recorded data Christina Zavou, Antria Kkoushi, Achilleas Koutsou, Chris Christodoulou Dynamical properties of LFPs from mice with unilateral injection of TeNT Eleonora Vannini, Matteo Caleo, Santi Chillemi, Angelo Di Garbo Functional data analysis of single-trial auditory evoked potentials recorded in the awake rat Ondřej Pokora, Jan Koláček, Tzai-Wen Chiu, Wei Qiu Upozorneni: Neni-li v teto zprave vyslovne uvedeno jinak, ma tato E-mailova zprava nebo jeji prilohy pouze informativni charakter. Tato zprava ani jeji prilohy v zadnem ohledu ustavy AV CR, v.v.i. k nicemu nezavazuji. Text teto zpravy nebo jejich priloh neni navrhem na uzavreni smlouvy, ani prijetim pripadneho navrhu na uzavreni smlouvy, ani jinym pravnim jednanim smerujicim k uzavreni jakekoliv smlouvy a nezaklada predsmluvni odpovednost ustavu AV CR, v.v.i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institutes of CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, neither the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract; nor does it create any pre-contractual liability on the part of Institutes of CAS.

Dec. 31, 2017

Postdoctoral position in quantitative biological modeling

by William L. Kath

We are looking to fill a postdoctoral position in our department through an NSF-funded Research Training Program in Quantitative Biological Modeling. Could you please be so kind as to pass this information along to anyone who would be interested or might know of suitable candidates? Note that NSF requires postdoctoral fellows to be U.S. citizens or permanent residents. More details about the positions and the program are listed below. I've also linked a flyer suitable for printing and posting at http://people.esam.northwestern.edu/~kath/rtg_advertisement_2018.pdf Best regards, - Bill Kath ------------------------------------------------- Postdoctoral Fellowships in Quantitative Biological Modeling Department of Applied Mathematics, Northwestern University Overview: The Department of Engineering Sciences and Applied Mathematics is soliciting applications for a postdoctoral fellowship in quantitative biological modeling that will be available starting September 1, 2018. This position is part of a National Science Foundation Research Training Grant (NSF-RTG). Duties: The postdoctoral fellow will conduct research on the quantitative modeling of biological systems and will teach three quarter courses per year in the department. The position will typically be for three years. The postdoctoral fellow will additionally participate in RTG-related training and career development activities. Environment: The postdoctoral fellow will be part of an interdisciplinary environment focusing on current problems in experimental and computational biology. The fellow will gain experience from training in mathematical modeling, numerical methods, and modern data analysis/statistical tools relevant to biological problems. Research internships outside of Northwestern will broaden the fellow's perspectives. The fellow's research will be mentored by faculty from both applied mathematics and a biological discipline. Ongoing collaborations exist with faculty in Neurobiology, Molecular Biosciences, Environmental Engineering and Preventive Medicine, and additional areas of interest are welcome. An overall goal of the program is to broaden computational biological modeling in the department and at Northwestern. Requirements: Applicants must be U.S. citizens or permanent residents. Interested candidates should submit a curriculum vitae, three reference letters (one addressing teaching qualifications) and brief research and teaching statements online at the URL: https://openposition.mccormick.northwestern.edu/apply/index/NjY= If desired, one or two representative publications may also be submitted. For full consideration applications should be received by January 15, 2018. Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes including veterans and individuals with disabilities. Women and minorities are encouraged to apply. Inquiries about the position may be directed to: Hermann Riecke Engineering Sciences and Applied Mathematics Northwestern University 2145 Sheridan Road Evanston, IL 60208-3125 Phone: (847) 491-3345 Email:h-riecke@northwestern.edu http://www.mccormick.northwestern.edu/applied-math/ -- William L. Kath, Professor Engineering Sciences and Applied Mathematics McCormick School of Engineering, Northwestern University 2145 Sheridan Road, Evanston, IL 60208-3125 Phone: 847-491-8784 Fax: 847-491-2178

Dec. 30, 2017

Direct PhD Track - Brain Sciences: Computational and Information Processing

by Nili Vershov

*Direct PhD Track* *Brain Sciences: Computation and Information Processing* Now Accepting Applications from International Students! *Submission Deadline: February 1st, 2018* *For more information:* https://elsc.huji.ac.il/phd-program-computational-neuroscience -- *Nili Vershov* *Ph.D Program C**oordinator * *Edmond and Lily Safra Center for Brain Sciences* *The Hebrew University of Jerusalem* *Tel: +972-26584899 <+972%202-658-4899>* *Cell: +972-507858847 <+972%2050-785-8847>* ------------------------------ This message contains information which may be confidential and privileged. Unless you are the intended addressee (or authorized to receive for the intended addressee), you may not use, copy or disclose to anyone the message or any information contained in the message. If you have received the message in error, please advise the sender by reply and delete the message . To the extent contractual confidentiality obligations exist, this message and all information transmitted with it are designated "Confidential".

Dec. 27, 2017

Call for papers & tutorials: PRNI (Pattern Recognition in Neuroimaging) 2018

by Yuvaraj Rajamanickam (Dr)

******* please accept our apologies for cross-posting ******* -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- FIRST CALL FOR PAPERS AND TUTORIALS PRNI 2018: 8th International Workshop on Pattern Recognition in Neuroimaging to be held 12-14 June 2018 at the National University of Singapore, Singapore www.prni.org<https://webmail.ntu.edu.sg/owa/redir.aspx?C=zAsK2tVRfU-VqajW2fbnHXBsaTVlUtU…> - @PRNIworkshop - www.facebook.com/PRNIworkshop/<https://webmail.ntu.edu.sg/owa/redir.aspx?C=zAsK2tVRfU-VqajW2fbnHXBsaTVlUtU…> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The 8th International Workshop on Pattern Recognition in Neuroimaging (PRNI) will be held at the Centre for Life Sciences Auditorium, National University of Singapore, Singapore on June 12-14, 2018.Pattern recognition techniques are an important tool for neuroimaging data analysis. These techniques are helping to elucidate normal and abnormal brain function, cognition and perception, anatomical and functional brain architecture, biomarkers for diagnosis and personalized medicine, and as a scientific tool to decipher neural mechanisms underlying human cognition. The International Workshop on Pattern Recognition in Neuroimaging (PRNI) aims to: (1) foster dialogue between developers and users of cutting-edge analysis techniques in order to find matches between analysis techniques and neuroscientific questions; (2) showcase recent methodological advances in pattern recognition algorithms for neuroimaging analysis; and (3) identify challenging neuroscientific questions in need of new analysis approaches. Authors should prepare full papers with a maximum length of 4 pages (two column IEEE style) for double-blind review. The manuscript submission deadline is 04 April 2018, 11:59 pm SGT. Accepted manuscripts will be assigned either to an oral or poster sessions; all accepted manuscripts will be included in the workshop proceedings. Similarly to previous years, in addition to full length papers PRNI will also accept short abstracts (500 words excluding the title, abstract, tables, figure and data legends, and references) for poster presentation. Finally, this year PRNI has an open call for tutorial proposals. A tutorial can take a form of 2h, 4h or whole day event aimed at demonstrating a computational technique, software tool, or specific concept. Tutorial proposals featuring hands on demonstrations and promoting diversity (e.g. gender, background, institution) will be preferred. PRNI will cover conference registration fees for up to two tutors per accepted program. The submission deadline is also 04 April 2018, 11:59 pm SGT. Please see www.prni.org<https://webmail.ntu.edu.sg/owa/redir.aspx?C=zAsK2tVRfU-VqajW2fbnHXBsaTVlUtU…> and follow @PRNIworkshop and www.facebook.com/PRNIworkshop/<https://webmail.ntu.edu.sg/owa/redir.aspx?C=zAsK2tVRfU-VqajW2fbnHXBsaTVlUtU…> for news and details. ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents. Towards a sustainable earth: Print only when necessary. Thank you.

Dec. 27, 2017

Columbia Workshop on Brain Circuits, Memory and Computation 2018

by Aurel A. Lazar

Columbia Workshop on Brain Circuits, Memory and Computation 2018 <http://www.bionet.ee.columbia.edu/workshops/bcmc/2018> BCMC 2018 March 15-16, 2018 Center for Neural Engineering and Computation <http://cnec.columbia.edu/> Columbia University, New York, NY, USA Overview The goal of the workshop is to bring together researchers interested in developing executable models of neural computation/processing of the brain of model organisms. Of interest are models of computation that consist of elementary units of processing using brain circuits and memory elements. Elementary units of computation/processing include population encoding/decoding circuits with biophysically-grounded neuron models, non-linear dendritic processors for motion detection/direction selectivity, spike processing and pattern recognition neural circuits, movement control and decision-making circuits, etc. Memory units include models of spatio-temporal memory circuits, circuit models for memory access and storage, etc. A major aim of the workshop is to explore the integration of various sensory and control circuits in higher brain centers. A Fruit Fly Brain Hackathon <http://www.bionet.ee.columbia.edu/hackathons/ffbh/2018> is being conducted in conjunction with the workshop. Workshop participants are welcome to attend the hackathon. Registration Registration is free but all participants have to register <https://bcmc2018.eventbrite.com/>. Thank you! Organizer and Program Chair Aurel A. Lazar <http://www.ee.columbia.edu/~aurel>, Department of Electrical Engineering, Columbia University. Program Overview (Confirmed Speakers) Misha B. Ahrens <https://www.janelia.org/lab/ahrens-lab>, Janelia Research Campus, Ashburn, VA. Davi Bock <https://www.janelia.org/lab/bock-lab>, Janelia Research Campus, Ashburn, VA. Claude Desplan <https://wp.nyu.edu/desplanlab/>, Department of Biology, New York University. Mark A. Frye <http://www.fryelab.net/>, Department of Integrative Biology and Physiology, University of California, Los Angeles. C. Giovanni Galizia <http://neuro.uni-konstanz.de/03team/content/galizia.html>, Department of Biology, University of Konstanz. Maria N. Geffen <https://geffenlab.weebly.com/maria.html>, Department of Otorhinolaryngology and Department of Neuroscience, University of Pennsylvania. Hokto Kazama <http://kazama.brain.riken.jp/index.php>, Riken Brain Science Institute, Tokyo. Donggen Luo <http://mgv.pku.edu.cn/?co=posts&ac=faculty&catalog=enpiintro&pname=en_Dongg…>, McGovern Institute for Brain Research, Peking University, Beijing. Thomas Nowotny <http://www.sussex.ac.uk/profiles/206151>, Department of Informatics, University of Sussex. Pavan Ramdya <https://ramdya-lab.epfl.ch/home>, Brain Mind Institute, EPFL, Lausanne. Aravinthan D.T. Samuel <https://scholar.harvard.edu/aravisamuel/home>, Department of Physics and center for Brain Science, Harvard University. Simon G. Sprecher <http://www.sprecherlab.com/simon-sprecher/>, Department of Biology, University of Fribourg. Seth Tomchik <http://www.scripps.edu/tomchik/>, The Scripps Research Institute Florida. Joshua T. Vogelstein <http://jovo.me/>, Dept. of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University. Scott Waddell <https://www.dpag.ox.ac.uk/research/waddell-group>, Department of Physiology, Anatomy and Genetics, University of Oxford. Anthony M. Zador <http://zadorlab.cshl.edu/>, Cold Spring Harbor Laboratory. Aurel http://www.bionet.ee.columbia.edu

Dec. 26, 2017

Announcing Okinawa/OIST Computational Neuroscience Course 2018

by Erik De Schutter

OKINAWA/OIST COMPUTATIONAL NEUROSCIENCE COURSE 2018 Methods, Neurons, Networks and Behaviors June 25 to July 12, 2018 Okinawa Institute of Science and Technology Graduate University, Japan 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 25th through July 12th, 2018 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) only; January 1 - February 3, 2018. Applicants will receive confirmation of acceptance in March. Like in preceding years, the 15th 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 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 provides 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: • Maxim Bazhenov (University of California San Diego, USA) • Michael Brecht (Bernstein Center for Computational Neuroscience Berlin, Germany) • Erik De Schutter (OIST) • Kenji Doya (OIST) • Shaul Druckmann (Janelia Research Campus, USA) • Karl Friston (Wellcome Trust Centre for Neuroimaging, UCL, UK) • Wulfram Gerstner (École Polytechnique Fédérale de Lausanne, Switzerland) • Michele Giugliano (University of Antwerp, Belgium) • Mitsuo Kawato (ATR, Japan) • Bernd Kuhn (OIST) • Kazuhisa Shibata (Nagoya University, Japan) • Olaf Sporns (Indiana University, USA) • Greg Stephens (OIST) • Tatjana Tchumatchenko (MPI for Brain Research, Frankfurt, Germany) • Krasimira Tsaneva-Atanasova (University of Exeter, UK) • Yoko Yazaki-Sugiyama (OIST)

Dec. 25, 2017

COSYNE 2018: Cosyne tutorial session, Travel grants, Registration

by Tomas Hromadka

==================================================== Computational and Systems Neuroscience 2018 (Cosyne) MAIN MEETING 01 - 04 March 2018 Denver, Colorado WORKSHOPS 05 - 06 March 2018 Breckenridge, Colorado www.cosyne.org ==================================================== IMPORTANT DATES Online registration is now open. Travel grant submission is now open. Hotel booking is currently open. Travel grant application deadlines Dec 31, 2017, 11.59PM PST (*Undergraduate* Travel Grant) Jan 17, 2018, 11.59PM PST (Other travel grants) ---------------------------------------------------- COSYNE ---------------------------------------------------- The annual Cosyne meeting provides an inclusive forum for the exchange of empirical and theoretical approaches to problems in systems neuroscience, in order to understand how neural systems function. The MAIN MEETING is single-track. A set of invited talks is selected by the Executive Committee, and additional talks and posters are selected by the Program Committee, based on submitted abstracts. The WORKSHOPS feature in-depth discussion of current topics of interest, in a small group setting. For details on workshop proposals please see below or visit Cosyne.org -> Workshops. Cosyne topics include but are not limited to: neural coding, natural scene statistics, dendritic computation, neural basis of persistent activity, nonlinear receptive field mapping, representations of time and sequence, reward systems, decision-making, synaptic plasticity, map formation and plasticity, population coding, attention, and computation with spiking networks. We would like to foster increased participation from experimental groups as well as computational ones. Please circulate widely and encourage your students and postdocs to apply. ---------------------------------------------------- COSYNE TUTORIAL SESSION ---------------------------------------------------- This year, Cosyne is hosting its first tutorial session. The tutorial on "Statistical models for neural data: from GLMs to latent variables" will be given by Jonathan Pillow on 01 March, before the main meeting starts. Space is limited. You can register for the tutorial when registering for the main meeting. For details on the tutorial and registration, see Cosyne.org -> Tutorial and Cosyne.org -> Registration. ----------------------------------------------- TRAVEL GRANTS ----------------------------------------------- Applications are now open for travel grants to attend the conference. Each awardee will receive at least $500 to help offset the costs of travel, registration, and accommodations. Larger grants may be available to those traveling from outside North America. Special consideration is given to scientists who have not previously attended the meeting, under-represented minorities, students who are attending the meeting together with a mentor, undergraduate students, and authors of submitted Cosyne abstracts. We currently offer five travel grant programs for New Attendees, Presenters, Mentors, Undergraduates, and Childcare travel grants. For details on applying, see Cosyne.org -> Travel grants. COSYNE SPEAKERS Tim Behrens (Oxford) Josh Berke (UCSF) Tiago Branco (UCL) Jessica Cardin (Yale) Claudia Clopath (Imperial) Marlene Cohen (Pittsburgh) Iain Couzin (Max-Planck) Carina Curto (Penn State) Ann Graybiel (MIT) Vivek Jayaraman (Janelia) Mate Lengyel (Cambridge) Joni Wallis (Berkeley) Byron Yu (CMU) ORGANIZING COMMITTEE General Chairs: Ilana Witten (Princeton) and Eric Shea-Brown (U Washington) Program Chairs: Linda Wilbrecht (Berkeley) and Brent Doiron (U Pittsburgh) Workshop Chairs: Laura Busse (LMU) and Ralf Haefner (U Rochester) Undergraduate Travel Chairs: Angela Langdon (Princeton) and Robert Wilson (U Arizona) Publicity Chair: Il Memming Park (Stony Brook) Development Chair: Michael Long (NYU) EXECUTIVE COMMITTEE Stephanie Palmer (U Chicago) Zachary Mainen (Champalimaud) Alexandre Pouget (U Geneva) Anthony Zador (CSHL) CONTACT meeting [at] cosyne.org COSYNE MAILING LISTS Please consider adding yourself to Cosyne mailing lists (groups) to receive email updates with various Cosyne-related information and join in helpful discussions. See Cosyne.org -> Mailing lists for details.

Dec. 23, 2017

EPSRC funded PhD in Computational/Mathematical Neuroscience (funded for UK students)

by James Rankin

*3 EPSRC funded PhD positions in Computational & Mathematical Neuroscience* UK students (or students who have spent last 3 years in UK) fully funded (fees and stipend) EU students partially funded (fees but no stipend) International students not eligible *Application deadline: 10th January 2018* Starting: September 2018 The studentships will provide funding for a stipend which is currently £14,553 per annum for 2017-2018. It will provide research costs and UK/EU tuition fees at Research Council UK rates for 42 months (3.5 years) for full-time students, pro rata for part-time students. * Cortical network models to understand differential input response properties during active and silent states* Supervisors: Dr James Rankin and Dr Mick Craig (Medical School, Exeter) http://www.exeter.ac.uk/studying/funding/award/?id=2903 * Determination of parameter dependencies across diverse populations of neuronal and excitable cells* Supervisors: Dr James Rankin and Dr Joel Tabak (Medical School, Exeter) http://www.exeter.ac.uk/studying/funding/award/?id=2932 *The neural circuitry mediating multisensory integration in Platynereis larvae* Supervisors: Dr James Rankin and Prof Gáspár Jékely (Living Systems Institute, Exeter) http://www.exeter.ac.uk/studying/funding/award/?id=2901 Apply through links above or contact pgrenquiries(a)exeter.ac.uk or j.a.rankin(a)exeter.ac.uk directly with any questions. -- http://emps.exeter.ac.uk/mathematics/staff/jar226

Dec. 21, 2017

Groningen Spring School on Cognitive Modeling 2018

by Jelmer Borst

Third Groningen Spring School on Cognitive Modeling – ACT-R, Nengo, PRIMs, & Accumulator Models – Date: April 9-13, 2018 Location: Groningen, the Netherlands Fee: € 250 (late fee after January 31 will be € 300) More information and registration: www.cognitive-modeling.com/springschool <http://www.cognitive-modeling.com/springschool> We are happy to announce the third Groningen Spring School on Cognitive Modeling (April 9-13, 2018). As in previous years, it will cover four different modeling paradigms: ACT-R, Nengo, PRIMs, and Accumulator models. It thereby offers a unique opportunity to learn the relative strengths and weaknesses of these approaches. See the attached flyer for more information about the paradigms. Each day will consist of four theory lectures, one on each modeling paradigm. Each paradigm also includes hands-on assignments. Although students are free to choose the number of lectures they attend, we recommend students to sign up for lectures on two of the paradigms, and complete the tutorial units for one of the paradigms. At the end of each day there will be a plenary research talk, to show how these different approaches to modeling are applied. The Spring School will be concluded with a keynote lecture and a conference dinner. This year we also offer the opportunity for project students to attend. The idea is that you have attended the spring school in an earlier year and now come back in the week of the spring school to work on your own modeling project under our supervision. Admission is limited, so register soon! We are looking forward to seeing you in Groningen! Niels Taatgen Jelmer Borst Marieke van Vugt Terry Stewart & Katja Mehlhorn

Dec. 20, 2017