October 2014 - Comp-neuro - lists.cnsorg.org

3rd Winter Q-Bio Mtg in HAWAII Feb. 2015 ***Registration is now open***
by Santamaria, Cookie 15 Oct '14

15 Oct '14

***REGISTRATION IS NOW OPEN*** https://www.regonline.com/qbio THE THIRD ANNUAL WINTER Q-BIO MEETING Quantitative Biology on the Hawaiian Islands February 17-20, 2015 http://w-qbio.org/ The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. The venue for 2015 is the Westin Maui<http://www.westinmaui.com/> Resort & Spa, which is located along the west coast of Maui. The resort is situated along a spectacular stretch of the famed Ka'anapali Beach. This oceanfront resort blends an endless array of activities and amenities with gracious aloha spirit, perfect for any Hawaiian meeting. Located beachfront with spectacular views of Lana'i and Moloka'i, The Westin Maui Resort & Spa is just minutes from Maui's many attractions, yet remains a world unto itself, where exclusive services, first-rate restaurants, cultured entertainment, and thrilling diversions satisfy every interest. This year we will select contributed talks from the submitted abstracts to be presented with the invited talks during the plenary sessions. Contributed talks will also be selected for parallel breakout sessions that commence in the late afternoon. 2015 CONFIRMED SPEAKERS: Uri Alon, Weizmann Institute Philip Campbell, Nature Michael Elowitz, California Institute of Technology Tim Elston, University of North Carolina Evonne Kaplan-Liss, Stony Brook University Galit Lahav, Harvard Medical School Wendell Lim, University of California, San Francisco Susan Lindquist, Whitehead Institute Jennifer Lippincott-Schwartz, National Institutes of Health Bernhard Palsson, University of California, San Diego Eva Maria Schoetz-Collins, University of California, San Diego Pamela Silver, Harvard Medical School Gurol Suel, University of California, San Diego Mary Teruel, Stanford University Olga Troyanskaya, Princeton University CONFERENCE ORGANIZERS: William Ditto, University of Hawaii at Manoa Hana El-Samad, University of California, San Francisco Jeff Hasty, University of California, San Diego Galit Lahav, Harvard University Eva-Maria Schoetz-Collins, University of California, San Diego Lev Tsimring, University of California, San Diego ***REGISTRATION IS NOW OPEN *** Registration fee covers conference venue, registration reception, banquet, coffee & snacks. EARLY BIRD REGISTRATION ($600 / $475 Student) DEADLINE: Saturday, December 20, 2014 REGULAR REGISTRATION ($700 / $575 Student) DEADLINE: Saturday, January 31, 2015 LATE REGISTRATION ($775 / $650 Student) After Saturday, January 31, 2015 REGISTRATION IS AVAILABLE AT: http://w-qbio.org/ HOTEL: A block of rooms has been reserved for registered conference participants at a negotiated rate starting at $209 per night plus tax at the Westin Maui<http://www.westinmaui.com/>. The rooms will be available soon on a first-come, first-served basis, so book early! CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 5th deadline. Abstract guidelines and submission information at: http://w-qbio.org/abstracts/ ABSTRACT DEADLINE: Wednesday, November 5, 2014 We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event. SPONSORED BY: UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology The University of Hawaii at Manoa UC San Diego Divisions of Biological Sciences and Engineering The Office of Naval Research Questions should be emailed to: coordinator(a)w-qbio.org<mailto:coordinator@w-qbio.org>

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Faculty Position in Computational Neuroscience at the University of California, Irvine
by Jeff Krichmar 15 Oct '14

15 Oct '14

Dear Computational Neuroscientists, The following job position may be of interest to many of you. ************************** University of California, Irvine Faculty Position in Computational Neuroscience The Department of Cognitive Sciences (www.cogsci.uci.edu) at the University of California, Irvine (UCI) invites applications for a faculty position at the Associate or Full Professor level. We are especially interested in candidates who use mathematical, computational, or robotics approaches to study the neural basis of cognition in any of these areas: (1) vision, hearing, and attention; (2) memory and decision-making; (3) learning and development; (4) language. Applicants whose research relates to human behavior are preferred. A strong record of publications and extramural funding is essential. Exceptional candidates at the Assistant Professor level will also be considered. The online application includes: A cover letter, CV, research and teaching statements, 3 recent publications, and contact information for 3-5 referees. Interested candidates can apply for the position at: https://recruit.ap.uci.edu/apply/JPF02452. To ensure full consideration, please complete the application by November 15, 2014. The University of California, Irvine is an Equal Opportunity/Affirmative Action Employer committed to excellence through diversity. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy. ************************** Best regards, Jeff Krichmar Department of Cognitive Sciences 2328 Social & Behavioral Sciences Gateway University of California, Irvine Irvine, CA 92697-5100 jkrichma(a)uci.edu http://www.socsci.uci.edu/~jkrichma

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Postdoctoral position in computational neuroscience at Numenta
by Subutai Ahmad 14 Oct '14

14 Oct '14

*POSTDOCTORAL POSITION IN THEORETICAL NEUROSCIENCE * *AND CORTICAL MODELING* *Numenta, Inc.* *About Numenta* Numenta was founded in 2005 to be a catalyst in the emerging field of machine intelligence. Its biologically inspired technology is based on a detailed and evolving theory of the neocortex first described in co-founder Jeff Hawkins’ book, On Intelligence. The current technology can be applied to anomaly detection in servers and applications, human behavior, and geo-spatial tracking data. Numenta is focused on understanding the computational principles behind the cortex in detail, and implementing practical systems that operate on those principles. For more details, please see www.numenta.com *Job description* Numenta has an immediate opening for a Postdoctoral Researcher. This individual will be a key member of our research group. He or she will work on significant extensions of Hierarchical Temporal Memory (HTM) theory and its implementations. Our current research efforts involve understanding cortical sensorimotor inference and control, and the role of thalamocortical pathways. Our models aim to build stable invariant representations of complex environments through active exploration, and are independent of sensory modality. Our problem domains span the range from artificial constrained worlds all the way to commercially driven applications. We seek researchers who passionately desire to build intelligent machines and impact the next generation of computing. The position carries full benefits and is for a one year term. An extension or a conversion to permanent employment is possible. We are located in Silicon Valley (Redwood City, CA). *Responsibilities* - Implement extensions to HTM theory - Test algorithms on a variety of problems and datasets - Characterize algorithm performance and suggest improvements - Write and publish papers in leading conferences and journals - Attend conferences and stay up to date with the latest relevant research - Be an active member of the NuPIC community (NuPIC is Numenta's open source HTM software) - Provide technical leadership to the rest of the organization *Desired qualifications* - Strong background in theoretical or computational neuroscience - Strong background in machine learning or machine intelligence - Established track record of leading edge research in computational neuroscience - Established track record of publications in leading peer reviewed conferences and journals - Excellent programming skills (Python or C++ preferred) - Hands on experience implementing large-scale learning algorithms or computational models - Preference given to candidates who have a deep understanding of HTM algorithms, cortical principles, and/or a working knowledge of NuPIC - Excellent verbal and written communication skills - Applicants should have, or expect to receive soon, a PhD (or have equivalent research experience) in computational neuroscience, machine learning, cognitive modeling, or a related discipline *How to apply* Qualified applicants should send the following to postdoc(a)numenta.com: - Cover letter describing their specific interest in Numenta. Please include any relevant experience with HTM algorithms or NuPIC. - Resume or CV, including list of relevant courses and published papers. Numenta is an equal opportunity employer supporting workforce diversity. IMPORTANT NOTE: Numenta is unable to consider postdoc applications from international researchers unless they are US Citizens, hold a Green Card, or are currently enrolled in a US University and eligible for OPT.

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Brain-Omics NIPS workshop: Call for contributions
by Gal Chechik 14 Oct '14

14 Oct '14

Call for contributions Workshop on *analyzing the 'omics of the brain* http://chechiklab.biu.ac.il/~gal/BrainOmics2014/ A workshop at the Twenty-Seventh Annual Conference on Neural Information Processing Systems (NIPS 2014) Montreal, QC, Canada, December 12, 2014. Important dates: * Oct 31, 2014* : Deadline for submission of extended abstracts Nov 10, 2014: Acceptance notification Dec 12, 2014: Workshop date WORKSHOP DESCRIPTION In the past few years, the field of molecular biology of the brain has been transformed from hypothesis-based experiments to high-throughput experiments. The massive growth of data, including measures of the brain transcriptome, methylome and proteome, now raises new questions in neurobiology and new challenges in analysis of these complex and vast datasets. While many of these challenges are shared with other computational biology studies, the complexity of the brain poses special challenges. Brain genomics data includes high-resolution molecular imagery, developmental time courses and most importantly, underlies complex behavioral phenotypes and psychiatric diseases. New methods are needed to address questions about the brain-wide, genome-wide and life-long genomic patterns in the brain and their relation to brain functions like plasticity and information processing. The goal of the workshop is to bring together people from the neuroscience, cognitive science and the machine learning community. It aims to ease the path for scientists to connect the wealth of genomic data to the issues of cognition and learning that are central to NIPS, with an eye to the emerging high-throughput behavioral data which many are gathering. We invite contributed talks on novel methods of analysis to brain genomics, as well as techniques to make meaningful statistical relationships to phenotypes. The target audience includes two main groups: people interested in developing machine learning approaches to neuroscience, and people from neuroscience and cognitive science interested in connecting their work to brain genomics. SUBMISSION INSTRUCTIONS Researchers interested in contributing should upload an extended abstract of 4 pages in PDF format to the Brain-omics submission web site https://easychair.org/conferences/?conf=brainomics2014 by Oct 31st, 2014, 11:59pm (time zone of your choice). No special style is required. Authors may use the NIPS style file, but are also free to use other styles as long as they use standard font size (11 pt) and margins (1 in). Relevant works that have been recently published or presented elsewhere are allowed, provided that previous publications are explicitly acknowledged. CONFIRMED INVITED SPEAKERS Nenad Sestan (Yale) Eran Mukamel (UCSD) ORGANIZERS Gal Chechik (BIU) Mark Reimers (VCU) Michael Hawrylycz (Allen institute)

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Special Issue on Cross-Frequency Coupling in Brain Networks
by Tjeerd Boonstra 14 Oct '14

14 Oct '14

Dear colleagues, We would like to draw your attention and cordially invite you to submit a manuscript to the Special Issue on Cross-Frequency Coupling in Brain Networks: Methodological Challenges and Functional Implications in BioMed Research International. Manuscripts are due on Friday, 5 December 2014. For more information and to submit a manuscript please see: http://www.hindawi.com/journals/bmri/si/897985/cfp/. We look forward to your contributions. Tjeerd Boonstra Ali Bahramisharif Andreas Daffertshofer Sylvain Baillet Cross-Frequency Coupling in Brain Networks: Methodological Challenges and Functional Implications Synchronous activity of oscillating brain networks plays a fundamental role in cognitive functioning. Cross‐frequency coupling (CFC) has been proposed to be the mechanism for interaction of local and global processes and hence to enable the integration of neural information processing across timescales. We invite investigators to contribute original research articles as well as review articles to stimulate the continuing efforts to understand the neural correlates of CFC, the methodological and mathematical prerequisites for reliable detection of CFC in experimental data, and the functional role of CFC in organizing the temporal dynamics of neural computation.

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PhD position in neuro-computational research of modeling emotions
by Julien Vitay 12 Oct '14

12 Oct '14

Several PhD (E 13 TV-L, 100%) positions are available at the Technical University of Chemnitz (Germany) in the Department of Computer Science. The positions are funded for three years. Among other fields of human-machine interactions, we are particularly interested in neuro-computational research of modeling emotions, particularly brain-inspired or brain-like solutions of the emotional system involving vision and audition. Please see http://crossworlds.info/jobposting/ -------------------- Prof. Dr. Fred H Hamker Artificial Intelligence & Neuro Cognitive Systems Department of Computer Science Chemnitz University of Technology Strasse der Nationen 62 D - 09107 Chemnitz Germany Tel: +49 (0)371 531-37875 Fax: +49 (0)371 531-25739 email: fred.hamker(a)informatik.tu-chemnitz.de www: http://www.tu-chemnitz.de/informatik/KI/

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Petition for European Researchers "They have chosen ignorance"
by Alessandro Torcini 11 Oct '14

11 Oct '14

Petition for European Researchers "They have chosen ignorance" Scientists from different European countries describe in this letter that, despite marked heterogeneity in the situation of scientific research in their respective countries, there are strong similarities in the destructive policies being followed. This critical analysis, highlighted in Nature and simultaneously published in a number of newspapers across Europe, is a wake-up call to policy makers to correct their course, and to researchers and citizens to defend the essential role of science in society. This letter can be signed here. The national policymakers of an increasing number of Member States, along with European leaders, have completely lost touch with the reality of research. http://openletter.euroscience.org/ In the media Italy Repubblica http://www.repubblica.it/economia/2014/10/08/news/scienziati_europei_contro… Ansa http://www.ansa.it/scienza/notizie/rubriche/ricerca/2014/10/09/ricercatori-… Micromega http://temi.repubblica.it/micromega-online/%E2%80%9Csenza-ricerca-non-si-es… Il Fatto Quotidiano http://www.ilfattoquotidiano.it/2014/10/09/tagli-alla-ricerca-la-lettera-de… Roars http://www.roars.it/online/hanno-scelto-lignoranza/ Uninews24 http://www.uninews24.it/mondo/5301-la-lettera-dei-ricercatori-contro-i-vert… France http://www.lemonde.fr/idees/article/2014/10/09/la-recherche-est-en-peril-il… Spain http://www.elmundo.es/ciencia/2014/10/08/54356cc2e2704e1d3e8b4597.html?cid=… http://elpais.com/elpais/2014/10/08/ciencia/1412764866_249154.html http://www.elperiodico.com/es/noticias/opinion/han-elegido-ignorancia-35861… http://www.elperiodico.cat/ca/noticias/opinio/han-elegit-ignorancia-3586110 Portugal http://www.publico.pt/n1672264 Greece http://www.tovima.gr/science/article/?aid=639347 http://www.tanea.gr/news/science-technology/article/5167615/nature-oi-polit… Poland http://www.rp.pl/artykul/9129,1147605-Apel-europejskich-naukowcow.html UK http://www.theguardian.com/science/occams-corner/2014/oct/09/they-have-chos… Belgium http://www.lesoir.be/674747/article/debats/cartes-blanches/2014-10-08/victi… See also http://www.euroscientist.com/blog/2014/10/09/pan-european-coordindated-grou… http://www.euroscientist.com/blog/2014/10/06/special-issue-research-activis…

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Post-doctoral research fellowship: modelling musical preference decisions
by Marcus Pearce 11 Oct '14

11 Oct '14

Dear All (with apologies for cross-posting), We seek to appoint a Post-doctoral Research Fellow at Queen Mary, University of London as part of an EPSRC-funded project <http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=EP/M000702/1>on predicting musical choices using computational models of cognitive and neural processing. The goal of the project is to understand the cognitive and neural processes involved in musical preference decisions using computational modelling that incorporates the structure of the music, the psychological state and traits of the listener and the listening context. The successful candidate will be involved in the design and implementation of the models, data collection from human listeners in behavioural and EEG experiments, analysing the data to test the model predictions, and writing up the results for publication in peer-reviewed journals. Start date: 5 January 2015. Duration: 14 months (until March 5 2016). Salary: £34,283. For further information and to apply see: http://music-cognition.eecs.qmul.ac.uk/postdoc.html Marcus -- Lecturer in Sound and Music Processing Queen Mary, University of London Mile End Road, London E1 4NS, UK Tel: +44 (0)20 7882 6207 Web: http://webprojects.eecs.qmul.ac.uk/marcusp Lab: http://music-cognition.eecs.qmul.ac.uk/

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Method development for coupled EEG-fMRI (1x Full EPSRC studentship)
by Etienne B. Roesch 10 Oct '14

10 Oct '14

Method development for coupled EEG-fMRI (1x Full EPSRC studentship) The goal of the project is to develop novel methods for the joint analysis of signals from electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), when they are obtained concurrently. Technological advances of the last 10 years make it possible for scientists to record both modalities concurrently, in what is now known as coupled EEG-fMRI. By simultaneously recording these two modalities, scientists can potentially say where and when neural activity is occurring, whereas previously researchers had to settle for one or the other. This engineering feat, however, has not yet been met with the ability to make use of the combination of these signals to infer more knowledge than would otherwise be gathered in separate experiments. Filling this gap is the ambition of the present project. This is a method project, which requires skills and knowledge in applied mathematics/statistics/physics and programming. One studentship is available, to join a research group in the remit of this project. Prior exposure to either/or EEG and fMRI is preferred, but training on both modalities will be provided. The emphasis of the studentship is on the development of novel analysis methods, but the successful candidate will have opportunities to join empirical work using EEG-fMRI. The student will be supervised by Dr. Etienne Roesch and receive support from Dr. Michael Lindner and Prof. Tom Johnstone, with R&D support from Brain Products. The CINN is host to a research-dedicated 3T Siemens TRIO, with a full license for sequence development, and a full suite of MR-compatible systems. Additionally, the student will be granted access to the cluster of NVIDIA Tesla GPUs and other facilities at CINN, as well as at the School of Systems Engineering. The University of Reading is ranked as one of the UK’s 20 most research-intensive universities and as one of the top 200 universities in the world (Times Higher Education 2013). Our campus was voted first in the Times Higher Education Student Experience survey and has a Green Flag Award. It is situated 25 minutes West of London. Reading University Students’ Union was voted the 6th best in the UK (National Student Survey 2012). Essentials: Commitment to academic research and personal development; Ability to work collaboratively; Effective interpersonal and communication skills, including writing to a high standard, document preparation for technical notes and journal papers; Experience of work in interdisciplinary settings; Attention to details. Desirables: Self-guided work in developing statistical designs and approaches in research; Creative approach to problem solving; Ability to work independently; Experience in giving presentations and conveying complex ideas clearly. Eligibility: Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent in a relevant subject. Please note that due to restrictions on the funding this studentship is for UK/EU applicants only. Funding Details: Studentship will cover Home/EU Fees, pay the Research Council minimum stipend (£13,863 in 2014/15) for up to 3 years and include funding for international conferences. How to apply: To apply for this studentship please submit an application for a PhD in Cybernetics (full time) to the University – see http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx . In the section ‘Research proposal’, please upload or copy-paste your covering letter. When prompted as part of your online application, you should provide details of the funding you are applying for, quoting the reference GS14-68. Once you have submitted your application, you should receive an email to confirm receipt of your online application. Please forward this email, along with your covering letter and CV (as pdf), to Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk, by the application deadline. Application Deadline: Monday November 10th, 2014 (interviews on November 21st, 2014, Skype or in Reading) Further Enquiries: Please contact Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk. Kind regards, Etienne Save the world from email! http://emailcharter.org ––– Dr. Etienne B. Roesch Lecturer (Assistant Professor) in Cognitive Science University of Reading, UK http://doodle.com/MeetWithEtienne

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ModelDB open source code for HH model with time-depended ion concentrations
by Markus A Dahlem 10 Oct '14

10 Oct '14

** We made our source code from two recent papers and one accepted manuscript now available on ModelDB ** *The code simulates the Hodgkin-Huxley model with time-dependent ion concentrations.* Briefly, the Hodgkin-Huxley (HH) model has 4 dynamical variables. Including Na+,K+, and Cl- extra- and intracellular ion concentrations introduces 6 further variables. Various simple reduction techniques, such as adiabatic elimination, synchronization, mass conservation, and electroneutrality have been used to reduce this extended HH formalism to again only 5 dynamical variables, while the model still retains adequate biophysical realism. For example, bursting and cortical spreading depression (SD) can be simulated. The model conserves the HH action potential dynamics. See Refs. [1,2] The accession number for the HH model with time-dependent ion concentrations is 167714. http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=167714 Moreover, the ModelDB accession number for a wild-type and mutant SD model described in paper Ref [3] is 167715. http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=167715 The model can be further reduced to only 4 dynamic variables (without Cl-). For dynamic volume control and further features, please get in contact with me, see below. This models require XPP, which is freely available from: http://www.math.pitt.edu/~bard/xpp/xpp.html Refs [1] N. Huebel, E. Schöll, and M. A. Dahlem, Bistable dynamics underlying excitability of ion homeostasis in neuron models, PLOS Comp. Biology. 10, e1003551 (2014) [2] N. Huebel and M. A. Dahlem, Dynamics from seconds to hours in Hodgkin–Huxley model with time–dependent ion concentrations and buffer reservoirs (accepted PLoS Comp Biol, arXiv 1404.3031) [3] M. A. Dahlem, J. Schumacher, and N. Huebel. Linking a genetic defect in migraine to spreading depression in a computational model, PeerJ, 2:e379 (2014). -- Dr. Markus Dahlem Web: https://sites.google.com/site/markusadahlem Max Planck Institute for the Physics of Complex Systems Department Biological Physics Nöthnitzer Straße 38 01187 Dresden Germany and Humboldt-Universität zu Berlin AG NLD Cardiovascular Physics Robert-Koch-Platz 4 10115 Berlin Germany phone: +49 (0)351 871 2402 email: dahlem(a)physik.hu-berlin.de skype: markus.dahlem

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