July 2015 - Comp-neuro - lists.cnsorg.org

NEURON course and NSG Workshop at SFN 2015 meeting
by Ted Carnevale 13 Jul '15

13 Jul '15

Two events of particular interest to computational neuroscientists will be presented as satellite sessions to the 2015 SFN meeting in Chicago. Using NEURON to Model Cells and Networks Friday, Oct. 16 from 9 AM to 5 PM at a site in downtown Chicago This course provides a practical introduction to building and using models of neurons and networks with NEURON. Covered topics include basic concepts, workflow for building and using models, speeding up simulations with parallel hardware from multicore personal computers to massively parallel supercomputers, using Python with NEURON, and modeling reactive diffusion with the RxD class. Using the Neuroscience Gateway Portal for Parallel Simulation Saturday, Oct. 17 from 9 AM to noon at a site in downtown Chicago This workshop combines didactic presentations with hands on instruction on how to use the Neuroscience Gateway Portal (NSG) for parallel simulations. NSG eliminates most adminstrative and technical barriers to using high performance computing resources--it even gives away free CPU time. Simulators that are currently installed on NSG include NEST, PyNN, Brian, GENESIS3, NEURON, and MOOSE. Also available is FreeSurfer, a set of tools for analysis and visualization of structural and functional brain imaging data. Friday, Oct. 2, is the registration deadline for both of these events, but you should sign up early because space is limited. See https://www.neuron.yale.edu/neuron/courses for more information and links to registration forms. --Ted

1 0

Workshop at CNS2015 on Dopamine neurons and the circuits they participate in
by Canavier, Carmen C. 13 Jul '15

13 Jul '15

Title: Computational Models of Midbrain Dopamine Neurons and Dopaminergic Signaling Organizer: Carmen Canavier ccanav(a)lsuhsc.edu<mailto:ccanav@lsuhsc.edu> July 23, Prague, Room RB209 (subject to change) Description: This workshop features recent experimental and modeling work on SNc and VTA dopamine neurons in the context of addiction, Parkinson’s disease and schizophrenia. Time Speaker Title 9-9:30 Alexey Kuznetsov A model for VTA circuitry: toolbox for the study of addictions 9:30-10 Eleftheria Pissadaki From the axons of the SNc dopamine neurons to their dendritic processes: further clues to susceptibility in Parkinson's disease 10-10:30 COFFEE BREAK 10:30-11 Rebekah Evans T type calcium channels trigger a hyperpolarization induced after depolarization (HI-ADP) in SNc dopamine neurons 11-11:30 Andy Oster VTA Dopamine Neuron Dynamics: response to ramping applied currents 11:30-12:00 Carmen Canavier Dynamic Diversity of Dopamine Neurons 12:00-1:30 LUNCH BREAK 1:30-2 Guillaume Drion Potential functional implications of a hidden variability in SNc DA neuron excitability 2-2:30 Jinyoung Jang Spontaneous firing system in the midbrain dopamine neu- ron 2:30-3 Boris Gutkin VTA circuit models and nicotine/alcohol effects on DA dynamics 3-3:30 DISCUSSION AND CLOSING REMARKS

1 0

Workshop at CNS2015: Open Collaboration in Computational Neuroscience
by Padraig Gleeson 13 Jul '15

13 Jul '15

[Apology for cross-postings] Announcing a workshop at the CNS2015 meeting in Prague, Thursday July 23: Open Collaboration in Computational Neuroscience http://opensourcebrain.org/docs/Help/Meetings#CNS_2015 Building and analysing biophysically and anatomically detailed neuronal networks is a complex and time consuming task, which ideally involves researchers with a range of backgrounds and technical skills. However, most labs cannot expect to have all of these researchers present at any given time. This can lead to stalled projects, lost data and software and needless repetition of experimental and computational work. A number of initiatives have been started which address these issues. Some are creating public resources with freely available data to constrain such models. Others are using best practices from open source software development to encourage building and sharing of models in a collaborative environment. This workshop will serve as an informative introduction to these projects as well as a discussion forum for getting feedback and gathering requirements from the community for the developers of these initiatives. There are still a number of slots available for *5-10 minute lightning talks*, so if you are involved in a project in this area and wish to publicise it, please get in contact. *Confirmed speakers:* Jan Antolik (CNRS) Collaboration in neuronal modelling: model sharing, workflows and provenance Nicholas Cain (Allen Brain Institute) Resources for Open Collaboration at the Allen Brain Institute <http://www.brain-map.org/> Padraig Gleeson (University College London) NeuroML <https://neuroml.org/> & the Open Source Brain Initiative <http://opensourcebrain.org/> Adrian Quintana (University College London) Geppetto <http://www.geppetto.org/>: online visualisation & simulation for neuronal models Michael Sonntag (LMU München) The NIX Project: Comprehensive Storage of Neuroscience Data and Metadata <https://github.com/G-Node/nix> Matteo Cantarelli (MetaCell Ltd) OpenWorm <http://www.openworm.org/> Aurel A. Lazar (Columbia University) Neurokernel <http://neurokernel.github.io/>: An Open Source Platform for Emulating the Fruit Fly Brain Bill Lytton (SUNY Downstate Medical Center) ModelDB <http://senselab.med.yale.edu/ModelDB/> Eilif Muller (EPFL) Human Brain Project <https://www.humanbrainproject.eu/> resources for the integrative modelling community Shreejoy Tripathy (University of British Columbia) Open electrophysiology data and Neuroelectro.org <http://neuroelectro.org/> ----------------------------------------------------- Padraig Gleeson Room 321, Anatomy Building Department of Neuroscience, Physiology& Pharmacology University College London Gower Street London WC1E 6BT United Kingdom +44 207 679 3214 p.gleeson(a)ucl.ac.uk -----------------------------------------------------

1 0

postdoc in computational neuroscience
by Máté Lengyel 13 Jul '15

13 Jul '15

Postdoctoral Fellow in Computational Neuroscience University of Cambridge We are seeking a highly creative and motivated postdoctoral fellow (research associate or senior research associate) to work in the group of Máté Lengyel (http://learning.eng.cam.ac.uk/Public/Lengyel/) at the Computational and Biological Learning Lab, Department of Engineering, University of Cambridge to work on circuit- and systems-level of memory, in particular the interaction between recollective and familiarity-based forms of recognition memory. The project involves collaboration with Peter Dayan (Gatsby Computational Neuroscience Unit, UCL), and also Richard Henson (MRC Cognition and Brain Unit, Cambridge) providing direct access to relevant behavioural and imaging data. More broadly, the group studies learning and memory from computational, algorithmic/representational and neurobiological viewpoints. Computationally and algorithmically, we use ideas from Bayesian approaches to statistical inference and reinforcement learning to characterize the goals and mechanisms of learning in terms of normative principles and behavioral results. We also perform dynamical systems analyses of reduced biophysical models to understand the mapping of these mechanisms into cellular and network models. We collaborate very closely with experimental neuroscience groups, doing in vitro intracellular recordings, multi-unit recordings in behaving animals, human psychophysical, and fMRI experiments. The successful candidate will have a strong analytical background and demonstrable interest in theoretical neuroscience. They should have or be close to completion of a PhD or equivalent in computational neuroscience, physics, mathematics, computer science, machine learning or a related field. Previous experience in computational neuroscience is not required, but preference will be given to candidates with sufficient programming skills to run numerical simulations, or expertise with neural network models, analysis of dynamical systems, and Bayesian techniques. The position is funded for several years, with an initial one-year appointment and an expectation of extension to at least two years given satisfactory performance. Salary depends on experience and is in the range £28,695 - £48,743 p.a. Further information: http://www.jobs.cam.ac.uk/job/7261/ http://www.jobs.cam.ac.uk/job/7176/ For informal queries, please contact Mate Lengyel <m.lengyel(a)eng.cam.ac.uk>. Mate Lengyel -- Mate Lengyel, PhD Computational and Biological Learning Lab Cambridge University Engineering Department Trumpington Street, Cambridge CB2 1PZ, UK tel: +44 (0)1223 748 532, fax: +44 (0)1223 765 587 email: m.lengyel(a)eng.cam.ac.uk web: www.eng.cam.ac.uk/~m.lengyel

1 0

Re: [Comp-neuro] Postdoc position in Large-scale Neuronal Ensemble Recordings in Sensori-motor Cortices in Behaving Marmosets
by Nicholas Hatsopoulos 11 Jul '15

11 Jul '15

Postdoctoral Position in Large-scale Neuronal Ensemble Recordings in Sensori-motor Cortices in Behaving Marmosets A postdoctoral position is available starting in the fall of 2015 to characterize the spatio-temporal organization of sensori-motor cortical activity at multiple spatial scales associated with upper limb movements of behaving marmosets. This project involves high density multi-electrode array recordings as well as calcium fluorescence imaging from motor and somatosensory cortical sites in marmosets performing natural arm and hand movements. Facilities include a fully equipped electrophysiological laboratory with three 128-channel acquisition systems for multi-electrode recording and stimulation, calcium fluorescence imaging microscopes, and a camera-based, motion capture system. Expertise in multi-site, behavioral electrophysiology and/or calcium imaging is preferred. A strong mathematical, computational, or engineering background is also desirable. Applicants should send a CV and names and addresses of two or three references to Dr. Nicholas Hatsopoulos, Department of Organismal Biology, University of Chicago, 1027 East 57th Street, Chicago, IL 60637 or by e-mail to nicho(a)uchicago.edu<mailto:nicho@uchicago.edu>. Nicholas Hatsopoulos Professor Chair, Committee on Computational Neuroscience University of Chicago Culver Hall, Room 206 1027 East 57th street Chicago, IL 60637 773-702-5594 ________________________________

1 0

ICDL-EpiRob 2015 - registration open
by Benjamin Rosman 10 Jul '15

10 Jul '15

======================================================== REGISTRATION NOW OPEN IEEE ICDL-EPIROB 2015 The Fifth Joint IEEE International Conference on Development and Learning and on Epigenetic Robotics Brown University, Providence, Rhode Island, USA August 13-16, 2015 http://www.icdl-epirob.org/ Registration is now open at: http://www.tech.plym.ac.uk/SoCCE/CRNS/icdl-epirob//2015/registration.html In addition to the main conference, we will have both a preconference workshop and tutorial: Morning: "Introduction to Brains as Emergent Turing Machines" (Juyang Weng) Afternoon: "Mechanisms of learning in social contexts" (Michael Goldstein, Chen Yu) == Conference description The past decade has seen the emergence of a new scientific field that studies how intelligent biological and artificial systems develop sensorimotor, cognitive, emotional and social abilities, over extended periods of time, through dynamic interactions with their physical and social environments. This field lies at the intersection of a number of scientific and engineering disciplines including Neuroscience, Developmental Psychology, Developmental Linguistics, Cognitive Science, Computational Neuroscience, Artificial Intelligence, Machine Learning, and Robotics. Various terms have been associated with this new field such as Autonomous Mental Development, Epigenetic Robotics, Developmental Robotics, etc., and several scientific meetings have been established. The two most prominent conference series of this field, the International Conference on Development and Learning (ICDL) and the International Conference on Epigenetic Robotics (EpiRob), are now joining forces for the fifth time and invite submissions for a joint conference in 2015, to explore and extend the interdisciplinary boundaries of this field. == BABYBOT CHALLENGE We are excited to announce a new ICDL-EpiRob conference feature: the BABYBOT CHALLENGE. The goal of the challenge is to use the tools of developmental robotics to replicate and extend the key findings from one of three selected human-infant studies. These will be presented during a special session. == Keynote speakers Prof. Dare Baldwin, Dept. of Psychology, University of Oregon, USA Prof. Kerstin Dautenhahn, School of Computer Science, University of Hertfordshire, UK Prof. Asif Ghazanfar, Dept. of Psychology, Princeton University, USA == Program committee General Chairs: Matthew Schlesinger (Southern Illinois Univ.) Dima Amso (Brown University) Bridge Chairs: Jeffrey Krichmar (UC Irvine) Bertram Malle (Brown University) Program Chairs: Anne Warlaumont (UC Merced) Clemént Moulin-Frier (INRIA) Publications Chairs: Lisa Meeden (Swarthmore College) Publicity Chairs: Lola Cañamero (Univ. of Hertfordshire) Matthias Rolf (Osaka University) Benjamin Rosman (CSIR) Local chairs: David Sobel (Brown University) Thomas Serre (Brown University) Finance chairs: Clayton Morrison (University of Arizona) -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Please consider the environment before printing this email.

1 0

Postdoctoral Position in Cybersecurity, Fordham CIS
by Henry Han 08 Jul '15

08 Jul '15

*Postdoctoral Position in Cybersecurity, Fordham CIS* *We invite applications for a postdoctoral researcher position in Cybersecurity in the Department of Computer and Information Science.*This position requires a Ph.D. in Computer Science or a closely related area with a specialization in cybersecurity. Those with expertise in network security, software security, cyber-physical systems, computer forensics, wireless security, biometrics-based security, e-Systems Security, and related areas of cybersecurity are encouraged to apply. This postdoctoral researcher will conduct high-quality research in cybersecurity and teach courses for MS program in Cybersecurity. The selected candidate can apply and compete for a tenure track position that will be available next year. *How to apply:* Send a detailed CV, research statement, teaching statement, and a list of info of 3-5 references with e-mail addresses in a single pdf file to xhan9(a)fordham.edu (Dr. Henry Han). Include job-code “POSTDOC-Cybersecurity” in subject line. Review of applications will begin immediately and continue until the position is filled. The Department of Computer and Information Science is currently in the process of expanding its undergraduate and graduate programs in order to serve students entering the growing fields of computer science, information science, and interdisciplinary areas. Fordham's administration is committed to increasing the department's local and national distinction in research and science education. Additional new members will join the faculty in the coming years to build upon the faculty's wide range of expertise and to serve new programs. The faculty of the Department of Computer and Information Science represent a wide range of academic backgrounds, research and professional interests. Serving undergraduate majors in computer science, information science, and interdisciplinary programs in Fordham College at Rose Hill (Bronx), Fordham College at Lincoln Center (Manhattan), and the School of Professional and Continuing Education (all 3 campuses), the department also offers an MS program in Computer Science in the Graduate School of Arts and Sciences and an MS in Cybersecurity in the School of Professional and Continuing Studies. An MS program in Data Analytics is in its final process of development. In the thriving metropolis of New York, these programs are ideally situated for education and productivity in the computer and information sciences and industries. The department has a rich network of professionals and organizations, including loyal alumni, throughout the Metropolitan area, and students benefit from research, internship, and career opportunities afforded by the city's vast resources. Fordham University. With over 14,500 students in its 13 schools, Fordham's Carnegie classification is Research University (High Research Activity). U.S. News & World Report currently ranks Fordham 57th nationally, placing it among the Tier 1 universities. Fordham's New York City campuses in the center of Manhattan and the Bronx avail faculty and students of extraordinary resources for education, research, and service. Fordham offers its students a highly dedicated faculty, a productive research environment, emphasis on ethics and social justice, and respect for all individuals, religions, cultures, and creeds. Fordham University is an independent, Catholic University in the Jesuit tradition that welcomes applications from men and women of all backgrounds. Fordham University is committed to excellence through diversity and welcomes candidates of all backgrounds; it is an equal opportunity employer.

1 0

CFP: ICDM Workshop HealthMining 2015 and HISS Special Issue (Deadline: July 20, 2015)
by william 08 Jul '15

08 Jul '15

[Please accept our apologies if you receive multiple copies of this email] CALL FOR PAPERS (Submission Deadline: July 20, 2015) HEALTHMINING 2015 - The ICDM Workshop on Data Mining and Decision Analytics on Public Health and Wellness (URL: http://www.comp.hkbu.edu.hk/~healthmining2015/) In conjunction with the IEEE International Conference on Data Mining (ICDM 2015) AIMS and SCOPE For many years, data mining and decision analytics techniques have already been extensively applied to various domains, such as smart environments, social networks, marketing, and web technology. The focus of this workshop is mainly on the issues and challenges of data mining techniques with the purpose of improving human well-being and quality of life. It is expected that the workshop may increase the diversity of application areas that can benefit from data mining. At the same time, it is also desirable that the discussion and vision of this workshop would also offer further insights into, as well as new tools for, the issues of data collection, processing, system modeling, simulation and optimization arising from various public health topics. The objective of this workshop is to serve as a venue for researchers to discuss how data mining and analytics methods can contribute to improving public health quality in clinical, medical/biomedical, and healthcare systems in smart ways, including evidence-based medicine, personalized treatment and healthcare, assistive technology and active surveillance and control of diseases. In addition to mining statistical regularities, associations, or causalities from large-scale health-related datasets, it would be more desirable to further investigate how the results can effectively and efficiently support decision-making, system modeling, optimization, and simulation in various healthcare systems. TOPICS OF INTEREST - Large-scale data acquisition and management issues for public health - Social and other network-based analysis for public health - Medical big data mining and innovative applications - Mining risk patterns in medical data - Mental and physical health data integration - Biomarker discovery and biomedical data mining - Clinical data mining for practice knowledge building - Data mining from clinical decision-making, and practitioner reflection - Data mining from genetic data of diseases - Data mining for disease profiling and personalized treatment - Data mining for (active) syndromic surveillance - Data mining for infectious/chronic disease epidemiology and control - Data mining for exploring hidden patterns in clinical systems - Data mining for medical/biomedical, and healthcare systems - Data mining for assistive environments - Data modeling and information management forpervasive assistive environments - Data mining and knowledge modeling for wellness - Spatiotemporal data exploration and mining of diseases - Unstructured data mining in medicine and healthcare - Semantic data mining in medicine and healthcare - Scalable data integration in medicine and healthcare - Evidence-based decision-support systems - Healthcare knowledge abstraction, classification, and summarization - Healthcare knowledge computerization, execution, inference, and representation IMPORTANT DATES - Paper Submission Due: Jul 20, 2015 - Paper Notification Date: Sep 1, 2015 - Workshop Date: Nov 13, 2015 >>> SPECIAL ISSUE <<< Selected papers of the workshop will be invited for revision to be included in a special issue to be published in Health Information Science and Systems (URL: http://www.hissjournal.com/) ORGANIZING COMMITTEE - William K. Cheung, Hong Kong Baptist University, Hong Kong - Jiming Liu, Hong Kong Baptist University, Hong Kong - Parisa Rashidi, University of Florida, USA - Fei Wang, University of Connecticut, USA Department of Computer Science: http://www.comp.hkbu.edu.hk HKBU Faculty of Science: http://www.sci.hkbu.edu.hk Disclaimer: http://www.comp.hkbu.edu.hk/disclaimer

1 0

New computational challenge on Big Data and neurodegenerative diseases
by Neta Zach 07 Jul '15

07 Jul '15

Prize4Life, Sage Bionetworks and DREAM are proud to announce the launch of The DREAM ALS Stratification Prize4Life Challenge <https://www.synapse.org/#!Synapse:syn2873386/wiki/>. The prize, is a computational challenge inviting bioinformatics, statisticians, computation geeks and math geniuses to work on the PRO-ACT database and identify meaningful subgroups of ALS patients. The challenge offers a $28000 prize and journal partnership with Nature Biotechnology. You can read more about it here <http://www.jpost.com/Business-and-Innovation/Health-and-Science/Israel-base…> or join our Webinar about it on Wednesday <https://attendee.gotowebinar.com/register/2656120293543998721> July 8 at 11am EST. While most ALS patients die with 3-5 years, but some patients, like Stephen Hawking, survive much longer. What differentiates the Stephen Hawkings from the Lou Gehrigs? Is ALs one disease or several sub-disease? the challenge invite participants to devleop algorithms that can stratify the ALS patient population into meaningful subgroups with distinct features. You can read more about it here <http://www.jpost.com/Business-and-Innovation/Health-and-Science/Israel-base…> . A previous Challenge, the ALS Prediction Prize <http://www.innocentive.com/prize4life-announces-50000-als-prediction-prize-…> which ran in 2012, using only a small subset of the full database, led to the creation of solutions that are able to reduce by 20% the number of patients needed for effective ALS clinical trials, a millions of dollars reduction in the costs of each future ALS clinical trials and are used by several drug companies. Furthermore, the Challenge’s winning algorithms identified novel features of ALS pathology that are predictive of disease progression. The Challenge summary was published in Nature biotechnology <http://www.nature.com/nbt/journal/v33/n1/full/nbt.3051.html> and were also covered by Science News <http://news.sciencemag.org/brain-behavior/2014/11/crowdsourcing-project-pre…> , Science Translational Medicine <http://stm.sciencemag.org/content/6/264/264ec204.full> and a News and views piece in Nature biotechnology <http://www.nature.com/nbt/journal/v33/n1/full/nbt.3118.html>. The ALS Stratification Challenge aims to go beyond the prediction prize and bring us one step closer to personalized medicine- to accurately and effectively identify meaningful subgroups of diverse ALS patients and the predictive models and features specific to these subgroups. Winners will win $28000 and the winning submissions with be published with a journal partnership from Nature Biotechnology. You can read more- and Join!- here <https://www.synapse.org/#!Synapse:syn2873386/wiki/> Neta Zach, PhD | Chief Scientific Officer

1 0

PhD positions at LMU Munich
by Stefan Glasauer 06 Jul '15

06 Jul '15

Two PhD positions are available at Ludwig-Maximilians-Universität (LMU) München for a fixed term of 36 months, starting 1st September 2015. Both positions are linked to the research projects “Dynamic prior and contextual calibration”, which is a part of the newly funded German research group “active perception”. The project aims to uncover the mechanism underlying dynamic contextual calibration in multimodal environments, and to develop a general Bayesian framework describing the prior updating mechanisms in contextual calibration. In particular, we plan to focus on central tendency effects (for a review, see Shi, Church & Meck, 2013, Petzschner & Glasauer, 2015) in multimodal magnitude estimation. The project is expected to establish a general computational framework to examine whether the brain uses multiple modality-specific priors or an amodal prior in contextual calibration, and how the brain resolves inconsistencies among priors, as well as how action priors are taken into consideration in magnitude estimation. Successful candidates should have an excellent M.Sc. degree, or equivalent (or be currently working towards one) in a field of cognitive or computational neuroscience. Computational modeling and programming skills in MATLAB and R are essential. Good verbal and written communication skills in English, interest and some experience in multi-disciplinary research are highly desirable. Successful candidates will be paid according to German salary scale 65% TVL-13. One candidate will work in Department of Psychology, LMU under the supervision of Zhuanghua Shi, and the other candidate in the Center for Sensorimotor Research, LMU under the supervision of Stefan Glasauer. Applicants should send a completed application form along with a cover letter detailing their research experience and interests, a CV and two academic references electronically to either Zhuanghua Shi (shi(a)psy.lmu.de) or Stefan Glasauer (s.glasauer(a)lrz.uni-muenchen.de) The closing date for applications is August 1st, 2015. Shortlisted candidates will be invited for interview at the beginning of August. We regret that we may not be able to respond to all applications. Applicants who have not received an offer by the end of August 2015 should consider their application has been unsuccessful on this occasion. LMU Munich is an equal opportunity employer. Applications of women and disabled persons – given similar qualification – are preferred. Applicants with children are welcome. Part-time employment is possible in principle. ------------- Dr. Zhuanghua Shi Experimental Psychology, Department Psychologie LMU München Tel: (+49) 89 2180 5213 Fax: (+49) 89 2180 5211 Lab: http://www.psy.lmu.de/exp/mlab/

1 0