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Ph.D. and Master positions in theoretical neuroscience at the MPI for Brain Research

by Tatjana Tchumatchenko

Ph.D. and Master positions in theoretical neuroscience at the Max Planck Institute for Brain Research We are seeking undergraduate students interested in writing a Master thesis and also have open positions for Ph.D. Students to join our group "Theory of neural dynamics" at the Max Planck Institute for Brain Research lead by Dr. Tatjana Tchumatchenko. Our group studies how networks of neurons encode and decode sensory stimuli and how these functions are related to computations that underlie cognitive functions and behavior. We develop models to address linear and non-linear properties of neuronal networks and have ongoing collaborations with experimental labs where we analyze in vitro as well as in vivo data and develop appropriate models to explain the observed phenomena. Successful applicants should have a strong background in a quantitative field such as physics, mathematics or computer science and should be interested in an interdisciplinary exchange with other disciplines such as biology or medicine. Life science majors interested in quantitative modeling work are also encouraged to apply, particularly if they would like to combine experiments and theory in their Master or Ph.D. thesis work. We are looking for candidates with strong English skills and prior programming experience. In order to make teamwork in our group enjoyable and fun, the ideal candidate should have a strong work ethic and have demonstrated consistent self-motivation skills. Female students are particularly encouraged to apply. Prospective students should apply by sending an email to theoryneuraldynamics(a)gmail.com which includes * a letter of motivation, * CV, * and a copy of the current academic transcripts To make your motivation letter easier to write for you and more informative for us, please check the list of questions to be answered in your motivation letter at http://www.tchumatchenko.de/Opportunities.html Looking forward to your applications! Tatjana Tchumatchenko -- Dr. Tatjana Tchumatchenko Research group leader Theory of Neural Dynamics Max Planck Institute for Brain Research Max-von-Laue-Str 4 60438 Frankfurt am Main, Germany www.tchumatchenko.de

May 4, 2016

Collaborative Development of Data-Driven Models of Neural Systems: Janelia Farm Sept 18-12

by Padraig Gleeson

[Apology for cross-postings] Dear colleagues, We are pleased to announce a conference on: Collaborative Development of Data-Driven Models of Neural Systems September 18-21, 2016 Janelia Farm Research Campus, Virginia, USA Deadline for registration: 18th May Detailed computational models are critical for elucidating neuronal and network function. They enable different levels of description to be linked, a wide range of neurophysiological experiments to be interpreted and quantitative predictions to be made. These factors are important for understanding large-scale complex systems, like neural circuits; however, more extensive use and scaling up of these data driven models pose challenges in ensuring that models are scientifically rigorous, as well as accessible and usable by both theoretical and experimental researchers alike. This conference will bring together a range of experimentalists, theoreticians and neuroinformatics developers with the aim of facilitating a global, open infrastructure for collaborative model development in neuroscience. *Organizers* Padraig Gleeson, University College London Angus Silver, University College London *Invited Participants* Anton Arkipov, Allen Institute for Brain Science Giorgio Ascoli, George Mason University Upinder Bhalla, National Centre for Biological Sciences Avrama Blackwell, George Mason University Kevin Briggman, National Institute of Neurological Disorders and Stroke/NIH Dean Buonomano, University of California, Los Angeles Nicholas Cain, Allen Institute for Brain Science Claudia Clopath, Imperial College London Rosa Cossart, Institut de Neurobiologie de la Méditerranée Sharon Crook, Arizona State University Andrew Davison, Centre National de la Recherche Scientifique Erik De Schutter, Okinawa Institute of Science and Technology Shaul Druckmann, Janelia Research Campus/HHMI Chris Eliasmith, University of Waterloo Jeremy Freeman, Janelia Research Campus/HHMI Michael Hausser, University College London Jeanette Hellgren Kotaleski, Karolinska Institutet Fritjof Helmchen, University of Zurich David Kleinfeld, University of California, San Diego Jeff Magee, Janelia Research Campus/HHMI Robert McDougal, Yale School of Medicine Eilif Muller, École Polytechnique Fédérale de Lausanne Hanchuan Peng, Allen Institute for Brain Science Ruben Portugues, Max Planck Institute of Neurobiology Mark Schnitzer, HHMI/Stanford University Ivan Soltesz, Stanford School of Medicine Nelson Spruston, Janelia Research Campus/HHMI Misha Tsodyks, Weizmann Institute of Science Registration is free, but places are limited.*Registration closes 18th May 2016*. For more details and to apply for participation go to https://www.janelia.org/you-janelia/conferences/collaborative-development-d…. ----------------------------------------------------- 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 -----------------------------------------------------

May 4, 2016

MICCAI Challenge on Neural Circuit Reconstruction

by Jan Funke

Dear colleagues, We would like to draw your attention to the MICCAI challenge "CREMI: Circuit Reconstruction from Electron Microscopy Images" (http://cremi.org/) As of May 1st, the training phase of the challenge has opened. We provide three volumes with dense neuron and synapse segmentation, along with annotations for pre- and post-synaptic partners (http://cremi.org/data.html) The goal of this challenge is to evaluate algorithms for automatic reconstruction of neurons and neuronal connectivity from serial section electron microscopy data. The comparison is performed not only by evaluating the quality of neuron segmentations, but also by assessing the accuracy of detecting synapses and identifying synaptic partners. The challenge is carried out on three large and diverse datasets from adult Drosophila melanogaster brain tissue, comprising neuron segmentation ground truth and annotations for synaptic connections. A successful solution would demonstrate its efficiency and generalizability, and carry great potential to reduce the time spent on manual reconstruction of neural circuits in electron microscopy volumes. Follow us on Twitter for updates (https://twitter.com/cremi_challenge) and feel free to contact us at challenge(a)cremi.org. Regards, The CREMI organizers (Jan Funke, Stephan Saalfeld, Davi Bock, Srini Turaga, and Eric Perlman)

May 3, 2016

BMVA Workshop on "Vision for interaction: From humans to robots"

by Alessandra Sciutti

=============================================== VISION FOR INTERACTION: From humans to robots One Day BMVA symposium - London, UK on October 19, 2016 Website: www.bmva.org/meetings ================================================ **************** Keynote Speakers: **************** + Prof. Antonia Hamilton (UCL) and + Prof. Yiannis Aloimonos (Univ. of Maryland). **************** Abstract: **************** Since early infancy, the ability of humans at interacting with each other is substantially strengthened by vision, with several visual processes tuned to support prosocial behaviour. For instance, a natural predisposition to look at human faces or to detect biological motion is present at birth. More refined abilities as the understanding and anticipation of others' actions progressively develop with age, leading, in a few years, to a full capability of interaction based on mutual understanding, joint coordination and collaboration. A key challenge of robotics research nowadays is to provide artificial agents with similar advanced visual perception skills, with the ultimate goal of designing humanoid robots able to recognize and interpret both explicit and implicit communication cues embedded in human movements. These achievements pave the way for the large-scale use of Human-Robot Interaction based applications on a variety of contexts, ranging from the design of personal robots, to physical, social and cognitive rehabilitation. ******************* Call for contributions: ******************* In this highly interdisciplinary one-day workshop we aim at bringing together contributions from the fields of cognitive science, robotics, machine vision and artificial intelligence, to corroborate the discussion on the potential guidelines to design and develop biologically-inspired computational vision models that may favour a natural interaction between artificial systems and humans. Please submit a short abstract summarizing your contribution, you may include links or pointers to web-based illustrations, demonstration material or papers giving more details. The work can be in progress or recently published, in addition to novel research. If you would like to give a talk, please contact Noceti (nicoletta.noceti(a)unige.it ) and Sciutti (alessandra.sciutti(a)iit.it ) by email by July 6, 2016. Areas of interest include but are not limited to: Vision neuroscience for interaction Computational vision models Vision for Robotics and Artificial intelligence Human robot interaction Vision in Social sciences This workshop is supported by the European Project CODEFROR (FP7-PIRSES-2013-612555) ************** Important dates: ************** + July 6, 2016 Deadline for abstract submission October 19, 2016 + BMVA symposium at BCS (British Computer Society) in London, UK. *********** Chairs: *********** + Nicoletta Noceti (Università degli Studi di Genova) - + nicoletta.noceti(a)unige.it Alessandra Sciutti (Istituto Italiano di + Tecnologia) - alessandra.sciutti(a)iit.it

May 3, 2016

Postdoc position: Neural engineering and BMI in NYU

by Chen, Zhe

Dear colleagues Applications are now being accepted for a postdoctoral fellow position to combine experimental, computational and engineering techniques to study neural mechanisms of central pain circuits using rodent models. The applicant will work closely with Dr. Zhe (Sage) Chen and Dr. Jing Wang at the New York University School of Medicine, with cross-disciplinary training in computational neuroscience, rodent behavior and electrophysiology, optogenetics, and neural engineering (brain-machine interface). The applicant will have great opportunities to interact with a large and growing neuroscience community at the NYU campus, including the Neuroscience Institute (http://neuroscience.med.nyu.edu) Center for Neural Science (http://www.cns.nyu.edu) Department of Neuroscience & Physiology (http://neuro-physio.med.nyu.edu) Department of Psychiatry (http://psych.med.nyu.edu) and Department of Anesthesiology, Perioperative Care and Pain Medicine (http://www.med.nyu.edu/anes/home ). NYU Neuroscience community is also surrounded by other institutions in the greater New York metropolitan area (such as Columbia, Cornell, Rockefeller and Mount Sinai). The postdoc position is available immediately, and will be renewable up to 4 years depending on performance. Applications must have a PhD degree in Engineering (Biomedical or Electrical), Statistics, Physics or a related discipline. The desired applicant is expected to be highly motivated and work independently as well as cooperatively with other colleagues in all research projects. Ability to learn new techniques and resolve new research challenges is essential. Strong experiences in developing rodent or primate brain-machine interface (BMI) systems are desired. Previous training in animal behavior and optogenetics, in vivo neurophysiological recordings, are preferred but not required. Strong programming skills in C/C++ or hardware implementation experiences are a plus. To apply, please send an email along with (i) CV (with a complete list of publications); (ii) a cover letter describing research accomplishments and interests; (iii) the names and contact information of two to three references to: Dr. Zhe (Sage) Chen (zhe.chen3(a)nyumc.org<mailto:zhe.chen3@nyumc.org>) with a subject line “Postdoc application”. Best Zhe (Sage) Chen ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

May 2, 2016

PhD position: population coding in the retina

by Olivier Marre

A funded PhD position is available at the Vision Institute, Paris, to work with Olivier Marre on population coding in the retina. We have developed methods to record the activity of a large number (100-200) of ganglion cells, the output of the retina. The student will perform experiments and analyze data to understand how information can be coded in this activity. A particular emphasis will be put on the coding of trajectories of moving objects in different visual contexts. The research project is highly interdisciplinary. Applicants should have a quantitative background or some programming experience. A background in biology is welcomed but not required. The student will be trained to perform in vitro retina experiments. The Vision Institute ( http://www.institut-vision.org ) is a research center located in the center of Paris and dedicated to research on vision and vision diseases, with the aim of bridging the gap between academic, clinical, and industrial research. It is affiliated to Pierre and Marie Curie University. This PhD is funded as part of a project involving Drs Frédéric Chavane and Ivo Vanzetta (INT Timone, Marseille, France) and Dr Bruno Cessac (INRIA, Sophia-Antipolis). Collaborations with these labs will therefore be encouraged. The position should ideally start in October 2016. For more information, please contact Olivier Marre: olivier.marre(a)inserm.fr

May 2, 2016

2nd Call for Papers: IEEE RO-MAN 2016 Workshop on Neuroscience Methods in Human-Robot Interaction

by Burcu Ayşen Ürgen

IEEE RO-MAN 2016 Workshop on Neuroscience Methods in Human-Robot Interaction (New York City, 26-31st August, 2016) Neuroscience methods such as brain imaging are increasingly used to address research questions in robotics, robot-human communication and interaction. This workshop will provide an overview of state-of-the-art work at the intersection of human-robot interaction and human neuroscience, to show how cross-disciplinary collaboration can be a win-win, and to help increase communication between researchers from different yet complementary disciplines, with the hope of catalysing new ideas and collaborations. Neuroscientists with expertise in several topics of interest for RO-MAN 2016 <http://www.ro-man2016.org/> (e.g., embodiment, empathy, social cognition, body movements, gestures, facial expressions, anthropomorphism, learning and imitation, social presence, inference of human states, machine learning and brain-machine interfaces) will introduce the methods used, and present empirical work exemplifying their application to robotics, highlighting not only how such studies have led to insights on neural mechanisms of interaction, communication, and collaboration, but also how the findings inform the design and development of new robots, robot-human collaborative systems, interaction modalities and interfaces. We will solicit papers from the broader community that address these themes. Robotics and neuroscience both being active, rapidly developing, and high priority research areas, and the combination of expertise across disciplines holding great promise for advances in both theory and applications, the workshop will serve an important role by bringing together researchers coming from different backgrounds. Panel sessions will address challenges for interdisciplinary and novel research and discuss ideas for increasing synergy and impact future work. *SPEAKERS* Ayse P. Saygin, PhD (UC San Diego, USA) Emily S. Cross, PhD (Bangor University, UK) Thierry Chaminade, PhD (Institut de Neurosciences de la Timone, FRANCE) Susanne Quadflieg, PhD (University of Bristol, UK) James Thompson, PhD (George Mason University, USA) *WORKSHOP ORGANIZERS* Burcu A. Urgen, PhD (University of Parma, ITALY) Ayse P. Saygin, PhD (UC San Diego, USA) Emily S. Cross, PhD (Bangor University, UK) Workshop website: http://neurorobotics.ucsd.edu/ *CALL FOR PAPERS* We solicit full paper submissions from cognitive and social neuroscientists and human-robot interaction researchers with expertise in several topics of interest for RO-MAN 2016 including but not limited to embodiment, empathy, social cognition, nonverbal communication via body movements, gestures, facial expressions, anthropomorphism, learning and imitation, social presence, social knowledge, inference of human states, machine learning and brain-machine interfaces. The submitted papers are intended to include applications of various neuroimaging methods such as functional magnetic resonance imaging (fMRI), electroencephalography (EEG), magnetoencephalography (MEG), and transcranial magnetic stimulation (TMS) to topics of relevance to RO-MAN 2016. Observational and behavioural studies may be suitable as long as they are highly cross-disciplinary. Theoretical papers that address the theme of the workshop and RO-MAN 2016 may also be included. The expectation from submissions is to highlight not only how neuroscience studies involving robotics have led to insights on the human cognitive and neural mechanisms of interaction, communication, and collaboration, but also how the findings inform the design and development of new robots, robot-human collaborative systems, interaction modalities and interfaces. *EVALUATION* All submissions will be evaluated by a minimum of two reviewers. The reviewers will evaluate each submission based on how informative the study has been both to human neuroscience AND human-robot interaction as well as the quality of the research methodology. All accepted papers will be published in workshop proceedings. Each paper accepted for an oral or poster presentation has to be presented by one of the authors. *IMPORTANT DEADLINES* Full paper submissions due 05/15/2016. Notifications will be sent by 05/18/2016. Final versions will be submitted by 05/20/2016. *PAPER GUIDELINES* All full paper submissions should follow the guidelines specified in the main conference website, check here <http://www.tc.columbia.edu/conferences/roman2016/submissions/papers/>. *HOW TO SUBMIT* The papers should be emailed to neuroscience.robotics.workshop(a)gmail.com by the deadline: 05/15/2016. -- Burcu Aysen Urgen, PhD Email: burcu.urgen(a)gmail.com Website: http://www.burcuaysenurgen.com

May 2, 2016

Book: Bayes' Rule With Python

by James Stone

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.

April 30, 2016

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

_________________________________________________________________________ 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/ ==================================================================

April 29, 2016

Call for proposals to host the annual Computational Neuroscience (CNS) Meeting in 2018

by Tam, Nicoladie

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)

April 29, 2016