April 2016 - Comp-neuro - lists.cnsorg.org

15 PhD positions for PACE, an EU funded Innovative Training Network for understanding Perception and Action in Complex Environments
by Laurent Perrinet 19 May '16

19 May '16

Dear colleagues, PACE (Perception and Action in Complex Environments) is an Innovative Training Network funded by the Marie Sklodowska-Curie program of the European Union starting on April 1st, 2015. The network involves 10 academic and private full partners, from 6 European and associated countries (France, Spain, Italy, Netherlands, UK, Israel), plus 5 associated partners (private companies and public organizations). The network gathers a broad range of expertise from experimental psychology, cognitive neurosciences, brain imaging, technology and clinical sciences as well as transferable skills. The PACE network promotes interdisciplinary research and training in the field of human movement sciences with a strong emphasis on perception-action coupling in complex environments. We focus on changes of this coupling across lifespan and in pathological diseases affecting the nervous system. The goal is to train PhD students through collaborative research projects, international courses and workshops. -> 15 PhD positions, starting next fall, are offered across the different network sites. You can find a short description of the proposed PhD projects at the following link: http://www.int.univ-amu.fr/IMG/pdf/PACE_Table_positions.pdf Applications are welcome immediately and until the end of May (but some specific timing constraints may be enforced in some of the partners' sites: please get more information from local contacts). You will find further general information (sections 1 to 3), eligibility and application conditions (section 4) here: http://www.int.univ-amu.fr/-ITN-Marie-Curie-network-PACE Thanks for distributing this announcement to potential candidates, Laurent -- Laurent Perrinet - INT (UMR 7289)/CNRS http://invibe.net/LaurentPerrinet

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Book: Bayes' Rule With Python
by James Stone 30 Apr '16

30 Apr '16

I'd like to announce the publication of this book: Bayes' Rule With Python A Tutorial Introduction to Bayesian Analysis by JV Stone Reviews, synopsis, and table of contents can be found here: http://jim-stone.staff.shef.ac.uk/BookBayes2012/books_by_jv_stone/index.html regards, Dr James V Stone, Department of Psychology, University of Sheffield, UK.

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SSBSS 2016: Call for Oral Presentations/Posters: 9-13 July 2016, Volterra (Pisa) Tuscany, Italy - 3rd Int. Synthetic & Systems Biology Summer School - Early Application: May 26, 2016
by Giuseppe Nicosia 29 Apr '16

29 Apr '16

_________________________________________________________________________ Call for Participation (apologies for multiple copies) Please help forward it to other potentially interested attendees, thanks! _________________________________________________________________________ 3rd International Synthetic and Systems Biology Summer School - SSBSS 2016, 9-13 July 2016, Volterra (Pisa) - Tuscany, Italy ssbss.school(a)gmail.com <mailto:ssbss.school@gmail.com> http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss EARLY APPLICATION DEADLINE: May 26, 2016 http://www.taosciences.it/ssbss/#application-form The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Volterra Learning Center (Pisa - Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results (with Oral Talks and Posters), and to interact with their peers, in a friendly and constructive environment. SSBSS 2016 DEADLINES: Early Application: May 26, 2016 Notification Acceptance: from April 2 to 28 May 2016 Late Application: from May 27, to July 4th 2016 Notification Acceptance: from May 28th 2016 according to registration time Early Short Talk/Poster Submission: May 26, 2016 Notification Acceptance: from 2 April to 28 May 2016 Late Short Talk/Poster Submission: from May 27, to July 4th 2016 Notification of Decision for Oral/Poster Presentation: from May 28, 2016 according to submission time http://www.taosciences.it/ssbss/#application-form FINAL LIST OF SPEAKERS * Yaakov (Kobi) Benenson, Synthetic Biology Group@Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland Lecture 1: The practice of mammalian synthetic biology Lecture 2: Mammalian cell classifiers * Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA Lecture 1: Genome Editing Technologies and Therapeutic Modalities Lecture 2: Benchmark Circuits and Topological Properties * Edoardo Boncinelli, Universita’ Vita-Salute San Raffaele, Milano, Italy Lecture: TBA * John Cumbers, Founder SynBioBeta, Mountain View, CA, USA Lecture: Synthetic Biology: new tools for an industry at an inflection point. * Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA Lecture 1: Modularity in genetic circuits: Dream versus Reality Lecture 2: Engineering Modularity in Genetic Circuits * Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy Lecture 1: "Engineering and Control of Biological Circuits in Yeast" Lecture 2: "Engineering and Control of Biological Circuits in Mammalian Cells * Barbara Di Ventura, Synthetic Biology Group, BioQuant/DKFZ, Heidelberg, Germany Lecture 1: Using blue light to control protein localization in living mammalian cells Lecture 2: Using split inteins for protein engineering in living cells * Jonathan S. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA Lecture 1: "Discovering and Characterizing CRISPR effectors" Lecture 2: "Probing Biology with CRISPR Screening" * Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark Lecture 1: "Developing an Integrated Cell Factory Design Tool" Lecture 2: "Using Automated Laboratory Evolution to Optimize Cell Factories” * Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel Lecture 1: "Single Molecule Approaches for Studying Gene Expression in Intact Mammalian Tissues" Lecture 2: "Systems Biology of Stem Cell-Maintained Tissues” * Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy Lecture 1: "DNA Nanotechnology Tools and Reactions for Synthetic Biology" Lecture 2: "Nature-inspired DNA-based Nanodevices Next Generation Sequencing Workshop – Afternoon July 12th, 2016 * “How fast can we align sequences?” Mario Guarracino, CNR, Italy * “Advanced Bioinformatics tools for NGS” – TBC Luca Zammataro, Yale University, USA Tutorials: * “Detection and analysis of contaminating sequences in NGS sequencing data” Ilaria Granata, CNR, Italy * “Detection and interpretation of circular RNAs in RNA-seq experiments” Parijat Tripathi, CNR, Italy SSBSS 2016 DIRECTORS Diego Di Bernardo, TeleThon Institute of Genetics & Medicine - TIGEM and University of Napoli "Federico II", Italy Giuseppe Nicosia, University of Catania, Italy Luca Zammataro, Yale University, USA MORE INFORMATION ssbss.school(a)gmail.com <mailto:ssbss.school@gmail.com> http://www.taosciences.it/ssbss/ https://www.facebook.com/ssbss.school/ https://twitter.com/SchoolSsbss Social event(s): social tour and dinner in Florence. Please help us distributing in your circles (emails, blogs, and social networks) the call for participation and call for oral talks/posters for SSBSS 2016. Together we will make SSBSS a great event! See you in Tuscany in July! More Info: ssbss.school(a)gmail.com <mailto:ssbss.school@gmail.com> http://www.taosciences.it/ssbss/ -- Giuseppe Nicosia, Ph.D. Associate Professor of Computer Engineering Dept of Mathematics & Computer Science University of Catania Viale A. Doria, 6 - 95125 Catania, Italy P +39 095 7383048 nicosia(a)dmi.unict.it http://www.dmi.unict.it/nicosia ================================================================== 3rd International Synthetic & Systems Biology Summer School - SSBSS 2016 * Biology meets Computer Science & Engineering * July 8-14, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/ssbss/ ================================================================== 2nd International Workshop on Machine learning, Optimization & big Data - MOD 2016 August 26-29, 2016 - Volterra (Pisa), Tuscany, Italy http://www.taosciences.it/mod/ ==================================================================

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Call for proposals to host the annual Computational Neuroscience (CNS) Meeting in 2018
by Tam, Nicoladie 29 Apr '16

29 Apr '16

Call for proposals to host the annual Computational Neuroscience (CNS) Meeting in 2018 The Organization for Computational Neurosciences (OCNS, http://www.cnsorg.org ) requests proposals from candidate local organizers to organize the CNS meeting in 2018 in a location outside of Europe, preferably in North or South America. Groups or individuals interested in organizing the CNS*2018 meeting should submit a proposal with consideration of the extensive on-line information ( http://www.cnsorg.org/cns-2018-local-organizer ) and using the on-line templates provided as a guide. The OCNS board members will select/discuss the different proposals, contact the potential local organizers for more information if necessary and come to a timely agreement between OCNS and potential local organizers. Proposals should be emailed to the OCNS president at president(a)cnsorg.org<mailto:president@cnsorg.org> no later than June 15th, 2016. Decisions are expected to be conveyed to potential organizers in July 2016. Astrid Prinz (OCNS President)

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Parallel Simulation with NEURON
by Ted Carnevale 28 Apr '16

28 Apr '16

A few seats remain available in the course Parallel Simulation with NEURON that we will be presenting at HHMI|Janelia Saturday, June 25 - Monday, June 27. This course is designed for users who already know how to write hoc or Python code for NEURON and now want to adapt existing models, or create new ones, that can be simulated on parallel hardware. Special attention will be paid to strategies for debugging, and measuring and improving performance. Registration is subject to approval by the course's faculty. The registration deadline is Friday, May 20, 2016. For more information and the online application form, see http://www.neuron.yale.edu/neuron/static/courses/summer2016/summer2016.html --Ted

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Fully funded PhD position, University of Genoa, Italy - "Visuo-haptic sensorimotor models"
by Silvio P. Sabatini 28 Apr '16

28 Apr '16

===================================================================== Applications are invited for one full-time PhD studentship (with scholarship) for a period of 3 years, at the Department of Informatics, Bioengineering, Robotics, and System Engineering, University of Genoa, Italy. ===================================================================== The position will start on Nov 1st, 2016 on the following research project: ACTION-PERCEPTION TRANSFER IN VISUAL AND VISUO-HAPTIC BEHAVIOR _Deadline for Applications: June 10th, 2016_ Experiencing the sensory feedback gained from movements allows us to learn the contingencies and correlations between actions and sensory events. Accordingly, sensing "educates" motor action, but, conversely, and more elusively, motor practice can "educate" sensing. The proposed research aims at investigating the interplay between action and perception at different levels: (1) modelling early action-perception transfer in visual feature extraction (cf. neural coding of visual properties) and perceptual judgement processes (decoding stages); (2) experiments on bidirectional perceptual-action influence - including the development of systems and devices that integrate vision and haptics; (3) applications in neuromotor and cognitive rehabilitation, in which action is used to educate perception and perception is used to educate action. The project will provide the opportunity to work on neural modeling, visual and visuo-haptic psychophysics, and robotics. Experimental, modeling, and theoretical approaches might be pursued with a different accent according to personal attitude. * HOW TO APPLY Candidates must have: - University degree at M.Sc. level (or expect to obtain it by October 31st, 2016) in Bioengineering, Computer Science, Physics, or related disciplines; - attitude for problem solving and interest in experimental work; - essential skills comprise Matlab and/or C/C++/C# or Python programming. Online application is possible till June 10th, 2016 (at noon) Italian time Full details on the call and the application procedure are available at: http://www.studenti.unige.it/postlaurea/dottorati/XXXII/ENG/ http://phd.dibris.unige.it/biorob/index.php/how-to-apply Prospective students, please contact: Silvio P. Sabatini (silvio.sabatini(a)unige.it) or Vittorio Sanguineti (vittorio.sanguineti(a)unige.it), providing your CV and qualifications, the name and contact details of two references, and a description of your research interests. * WHERE The research will be conducted jointly at "The Physical Structure of Perception and Computation (PSPC) Lab", and the "Neuro-engineering and Neuro-robotics lab (NEUROLAB)", led by Silvio P. Sabatini and Vittorio Sanguineti, respectively. PSPC-Lab has a long-standing expertise in visual coding and multidimensional signal representation, robot perception and computer vision. In the last years, the lab's research activity focused on the analysis of the structural mechanisms of visuo-spatial cognition, responsible for orienting and interacting in the 3D space. NEUROLAB (http://www.neurolab.dibris.unige.it/) focuses on experimental studies on neural control of movement, in normal and pathologic conditions. Recent activity aimed at investigating the computational basis of motor skill learning, and how this process can be facilitated by robots and other interactive technologies. Our labs are located in Genoa, a small beautiful town in northernItaly, both from historical (its historical center is the largest of Europe) and naturalistic point of view (sea and mountains coexist creating a unique landscape). Genoa is only 1.30h away from Milan by train and connected by plane to Rome (1.00h), London (2h) and Paris (1.30h). Regards, -- --------------------------------------------------------------------- Silvio P. SABATINI, PhD [PSPC Research Group] Professor of Bioengineering DIBRIS - University of Genova | e_mail:silvio.sabatini@unige.it Via Opera Pia, 11A | phone: +39 010 3532092/3532794 I-16145 Genova (ITALY) | fax: +39 010 3532289/3536533 URL:http://pspc.unige.it --------------------------------------------------------------------- "Imagination is more important than knowledge..." [Albert Einstein]

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PhD Studentships in Computational Neuroscience at the University of Hertfordshire
by Torben-Nielsen, Benjamin 28 Apr '16

28 Apr '16

We welcome applications for a funded PhD position in the Biocomputation Research Group at the University of Hertfordshire. The successful applicant will work on a project related to the detailed modelling of neuronal dynamics arising through dendritic processing and/or the analysis of morphological and circuit data. Potential projects in the fields of neuroinformatics and computational neuroscience include (but are not limited to): - Analysis of neuronal morphology and micro-circuitry. - Simulation of development of neuronal morphologies and tissues. - Simulation of dendritic processing on hardware. - Sensory processing and behaviour generation in individual invertebrate neurons. - Development of experimental robot controllers based on dendritic computation. - Structural plasticity at the single neuron and micro-circuitry level. More project ideas can be found here: http://www.dendrites.club/Positions.html The successful candidate will have extensive programming experience, preferably in Python (and/or other programming languages depending on the precise project). Depending on the project, experience with parallel programming (MPI, ZMQ), meshing software (VTK, CGAL, ITK, ...), or statistical analysis in R or Python are an advantage. In addition, we greatly value curiosity and a personal motivation to find out how things work. We collaborate closely with leading experimentalists and theoreticians all over the world, such as Prof. Adrian Moore (RIKEN, Japan), Prof. Erik De Schutter (OIST, Japan) and Dr. Marylka Uusisaari (Erasmus Medical Center Rotterdam, The Netherlands). The student will be based in the Biocomputation Group (biocomputation.herts.ac.uk) at the University of Hertfordshire and will be supervised by Drs. Ben Torben-Nielsen and Volker Steuber to whom informal enquiries can be sent. Successful candidates are eligible for a research studentship award from the University (approximately GBP 14,250 per annum bursary plus the payment of the student fees). Application forms can be obtained from Mrs Lorraine Nicholls, Research Student Administrator, STRI, University of Hertfordshire, College Lane, Hatfield, Herts, AL10 9AB, Tel: 01707 286083, l.nicholls @ herts.ac.uk. The short-listing process will begin on 30 May 2016. Dr. Ben Torben-Nielsen Senior Lecturer (Assistant professor) Biocomputation Group University of Hertfordshire, UK

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PhD Position: NEUROPHYSIOLOGY and BEHAVIOUR
by Andrea Burgalossi 28 Apr '16

28 Apr '16

PhD Position: NEUROPHYSIOLOGY and BEHAVIOUR The lab of Andrea Burgalossi at the Werner Reichardt Centre for Integrative Neuroscience (CIN) in Tübingen is looking for PhD candidates in the field of Neurophysiology and Behaviour Research in our lab focuses on the cellular basis of behavior. We employ a combination of anatomical and electrophysiological techiques for studying how defined neural circuits contribute to sensory and high-level representations of the external world. Possible PhD projects will involve the use of state-of-the-art in vivo electrophysiology techiques, in combination with anatomical methods for neural circuit mapping (please see www.burgalossilab.com or contact Andrea Burgalossi for more details). Previous experience with electrophysiological methods is desirable, but not essential. Analytical and programming skills are a plus. Applications should contain a CV and names of at least two referees. Please send your application electronically to andrea.burgalossi(a)cin.uni-tuebingen.de. More info at http://burgalossilab.com/ http://www.cin.uni-tuebingen.de/ SELECTED PUBLICATIONS Burgalossi et al., Neuron (2011) 70:773-86 Tang et al, Nature Protocols (2014) 9:2369-81 Tang et al., Neuron (2014) 84:1191-7 Ray et al., Science (2014) 343:891-6 Diamantaki et al., Current Biology (2016) 26:536-41 -- Andrea Burgalossi, PhD Cellular and Synaptic Basis of Behaviour Werner Reichardt Centre for Integrative Neuroscience (CIN) Otfried-Müller-Straße 25 72076 Tübingen Tel: 0049-(0)7071 / 29 - 88797 Fax: +49-(0)7071 / 29-25006 Lab web: burgalossilab.com CIN web: http://www.cin.uni-tuebingen.de

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Fully funded PhD position, University of Birmingham, UK - Human movement
by Chris Miall 27 Apr '16

27 Apr '16

Please bring this fully-funded 3-year PhD studentship to the attention of your students: Title: Quantification of motor performance in patients with impaired upper limb movements Supervisors: Chris Miall and Joe Galea,  Place: School of Psychology, University of Birmingham, UK There is growing need for accurate quantification of performance in patients with impaired upper limb movements. This arises from the need to assess recovery of movement following neurosurgery and stroke and to underpin a stratified approach to rehabilitation. We have recently developed methods to assess upper limb movements in a 2D workspace, using the resulting “performance map” to guide stroke rehabilitation. We have also developed methods to link the patients’ performance to muscle activation patterns. We now want to extend this work into 3D, to allow assessment of a broader range of movements, closer to normal activities, and in a shorter period of assessment. In addition, we wish to extend from stroke to assessment of functional recovery after neurosurgery, as a prelude to testing enhancement of recovery with brain stimulation: this would include patients with surgical repair of traumatic injury (road traffic accidents). Finally, we aim to extend our methods to link performance to muscle activation patterns in these continuous movements, in order to better understand the underlying deficits in motor control. The project will make use of a state-of-the-art 3D robotic arm, and assess performance by developing a 3D tracking task, in which a subject’s motor ability is progressively expanded from an initial slow and central focus to regions needing more extended limb postures and faster movement. An assistive algorithm in which the force-controlled robot guides movement towards the target will be used to help patients overcome weak and unstable movement, while still allowing assessment of performance speed, direction and stability. Actions in the robot-assisted task will be compared with free movement tracking in a virtual reality environment, with limb movements captured by existing motion tracking systems, but this motion tracking will ultimately be possible with a device such as the Microsoft Wii or smartphone. The comparisons will inform the potential to translate the assessment from the lab based robotic systems to the bedside. The outcome will be a set of diagnostic tests that deliver accurate quantification of upper limb movement control, suitable for triage of rehabilitation and for assessment of progressive recovery. The project is suited for students with an excellent first degree in neuroscience, engineering, robotics, or computer science. Masters training would also be advantageous. Experience in programming (Matlab or C) would be very valuable, and an interest in working with patients is important. There is studentship funding available for three years from the EPSRC, for UK or EU students only. Please contact Chris Miall (r.c.miall(a)bham.ac.uk<mailto:r.c.miall@bham.ac.uk>) or Joe Galea (j.galea(a)bham.ac.uk<mailto:j.galea@bham.ac.uk>) for further information or use FindaPhD: https://www.findaphd.com/search/ProjectDetails.aspx?PJID=74850 Deadline for application is 20-MAY-2016. ---------------------------------------------------------- Professor R.C. Miall Tel +44 (0)121 414 2867 School of Psychology, Fax +44 (0)121 414 4897 University of Birmingham, Mobile: +44 (0)7709 586997 Edgbaston, Email: r.c.miall(a)bham.ac.uk<mailto:r.c.miall@bham.ac.uk> Birmingham B15 2TT UK Web: http://prism.bham.ac.uk ----------------------------------------------------------

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PhD position in Neural Data Science / Retina
by Philipp Berens 27 Apr '16

27 Apr '16

The labs of Philipp Berens (www.berenslab.org) and Thomas Euler (www.eulerlab.de) at the Center for Integrative Neuroscience (CIN) at the Eberhard-Karls-University of Tübingen are offering a PhD position (TV-L E13 65%) to be filled as soon as possible, with funding for 3 years. The successful candidate will combine experimental and computational approaches to study *neuronal cell type specific computations* in the mouse *retina*. The goal of the project is to provide an account of how the functional response properties of selected ganglion cell types arise from their anatomical structure, connectivity and dendritic integration properties. We envision a highly interdisciplinary project, where the successful candidate will perform state-of-the-art optical imaging and electrophysiological recordings and use computational approaches to analyze their data. The CIN offers a stimulating interdisciplinary scientific environment where research is carried out at all levels of neuroscience. The two labs are also part of the Institute for Ophthalmic Research (Eye Hospital Tübingen) and affiliated with the Bernstein Centre for Computational Neuroscience (BCCN). Furthermore, the project will be performed in collaboration with the lab of Tom Baden at the University of Sussex, UK (www.badenlab.org). We offer employment with a salary and social benefits based on the collective agreement for public service employees in the academic and science sector, TV-L. The Eberhard-Karls-University of Tübingen promotes gender equality and therefore particularly encourages female scientists to apply. Preferential status will be given to handicapped persons, if equally qualified. Requirements: • Background in statistics, machine learning and data analysis • Experience with electrophysiology and/or two-photon imaging or a strong desire to learn these techniques • Programming experience in Python, Matlab, R or similar • Strong quantitative skills Interested applicants should contact Dr. Philipp Berens (philipp.berens(a)uni-tuebingen.de) providing: • a curriculum vitae • a one-page description of past research experience & future research interests • a one-page description of the motivation for applying to this position • names of at least two people that could provide letters of reference Please compile your application in one single PDF-file. -- University of Tübingen http://philippberens.wordpress.com http://www.bethgelab.org

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