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

NeuroMorpho.Org v7.2 released July 19th, 2017

by NeuroMorpho Administrator

Dear colleagues, We’re pleased to announce the July 19, 2017 release of Version 7.2 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 7721 reconstructions from 83 new datasets. The repository now provides access to 70,025 cells and passed 7 million downloads in 163 countries. Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data and other updates. The literature coverage was also updated to include publications through June 2017. We are continuously grateful to all the data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021>

July 21, 2017

8th NeuralEnsemble CodeJam workshop

by Andrew Davison

Dear colleagues, You are invited to participate in the 8th NeuralEnsemble CodeJam workshop, which will take place 13th-15th September 2017 in Lausanne, Switzerland. http://neuralensemble.org/meetings/CodeJam8/ The goal of the CodeJam is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics, by bringing together researchers, students and engineers to share ideas, present their work, and write code together. Mornings are dedicated to invited and contributed talks, leaving the afternoons free for discussions, tutorials and code sprints. CodeJam #8 is sponsored by the Human Brain Project Best regards, Andrew -- Andrew Davison, PhD Unité de Neurosciences, Information et Complexité (UNIC) Centre National de la Recherche Scientifique 1, avenue de la Terrasse 91198 Gif sur Yvette France Tel: +33 1 69 82 34 51 http://www.andrewdavison.info/

July 21, 2017

PhD studentship in Computational Neuroscience/Machine Learning

by Vassilis Cutsuridis

PhD Position in Computational Neuroscience/Machine learning MLearn Research Group School of Computer Science University of Lincoln UK Applications are invited for a PhD position in the MLearn Research Group at the University of Lincoln. Projects involve the development and simulation of models of neurons and neuronal networks hippocampal memory functions (Cutsuridis V, et al. (2010). Encoding and retrieval in the hippocampal CA1 microcircuit model. *Hippocampus*, 20(3): 423-446) <http://vassiliscutsuridis.com/docs/Journal_papers/CutCobGraHippo2010.pdf> and/or applications of machine learning (deep learning) techniques for the analysis of data. A description of our research interests and a list of publications can be found on our webpage (http://mlearn.lincoln.ac.uk/) Applicants should have excellent computational and numerical skills and a very good first degree in computer science, biology, maths, physics, neuroscience, or a related discipline. Successful candidates are eligible for a research studentship award from the University (GBP 14,553 per annum bursary plus payment of the student fees). This studentship is only open to UK and EU students. The ideal candidate should be highly motivated, technically skilled, a team player and driven to push forward the development of the next generation of deep associative memory neural-networks. Your written and spoken English skills should be excellent. As a PhD student, you may also have the opportunity to teach as a demonstrator in the School of Computer Science. Research in Computer Science at the University of Lincoln has been recognised as internationally excellent and world leading. The School of Computer Science provides a very stimulating environment, offering a large number of specialised and interdisciplinary seminars as well as general training and researcher development opportunities. The University is situated in Lincoln, two hours north of London. Please contact Dr Vassilis Cutsuridis (vcutsuridis(a)lincoln.ac.uk) or Prof. Stefanos Kollias (skollias(a)lincoln.ac.uk) for informal enquiries. If you’re interested in this position and you would like to apply, please send your CV, statement of research interests, three reference letters and a photo to Dr. Vassilis Cutsuridis: vcutsuridis(a)lincoln.ac.uk Applications will be assessed on a rolling basis, so please apply as soon as possible. Kind regards, Vassilis --- Dr Vassilis Cutsuridis School of Computer Science University of Lincoln Lincoln LN6 7TS U.K. Tel: +44 (0) 1522 83 5107 Email: vcutsuridis(a)lincoln.ac.uk Web: http://staff.lincoln.ac.uk/vcutsuridis Personal Web: http://www.vassiliscutsuridis.com/

July 20, 2017

Neuromodulation of Neural Microcircuits NM2 Conference 2017

by Ramaswamy Srikanth

We are delighted to announce the upcoming <https://nm2.epfl.ch> Neuromodulation of Neural Microcircuits (<https://nm2.epfl.ch>NM2) Conference 2017<https://nm2.epfl.ch>. The NM2 Conference will be held at the EPFL, Lausanne, Switzerland on the 18th and 19th of Sep. 2017 and at the Campus Biotech in Geneva, Switzerland on the 20th of Sep. 2017. Neuromodulators dynamically reconfigure neural microcircuits and shape brain states by controlling the function of neurons and glia, dendrites, and synapses. NM2 will bring together world-leading experts to: • Identify the state-of-the-art mechanisms of the neuromodulation of neural microcircuits • Illuminate various strategies enabling the measurement of neuromodulatory states in brain health and disease • Integrate knowledge to build a unifying view of the neuromodulation of different brain regions • Inform and attract new talent to drive forward neuromodulation research • Inspire future directions that will transform our understanding of the neuromodulation of brain function and dysfunction and therapeutic intervention NM2 has an exciting program<https://nm2.epfl.ch/page-145616-en.html> with a stimulating lineup of speakers<https://nm2.epfl.ch/page-145624-en.html>! Please mark your calendars to participate in shaping the future course of neuromodulatory research! Registration<https://nm2.epfl.ch/page-145625-en.html> includes coffee breaks, lunch, refreshments and poster sessions. PhD. students and postdocs are particularly encouraged to apply for several travel awards<https://nm2.epfl.ch/page-146294-en.html> by submitting poster abstracts<https://nm2.epfl.ch/page-146294-en.html>. Some abstracts will be selected for flash talks. Early bird registration is open until July 31st, 2017. Abstract submission is open until August 13th, 2017. We look forward to welcoming you at NM2 in beautiful Switzerland! Best regards from the scientific committee of NM2, Srikanth Ramaswamy Henry Markram Mriganka Sur Anita Disney Menahem Segal Michael Hasselmo Seung-Hee Lee Alexander Thiele Amy Arnsten [cid:CCBC7D9D-9041-4146-88BA-CC744BDBB811@epfl.ch]

July 20, 2017

PhD scholarship "Deep Learning in clinical neuroimaging", Charité Berlin

by Kerstin Ritter

Dear all, I am offering a PhD scholarship in "Deep Learning in clinical neuroimaging" at Charite Berlin, starting in October 2017 (initially for 2 years). See announcement below: _________________________________________ Deep Learning in clinical neuroimaging PhD scholarship (starting October 2017, initially for 2 years) At the Berlin Center for Advanced Neuroimaging and Bernstein Center for Computational Neuroscience (Charite), we are looking for a motivated and highly talented PhD student for various research questions within the interdisciplinary field of deep learning and clinical neuroimaging. In particular, we employ convolutional neural networks for finding new representations from neuroimaging data in order to predict disease conversion and future clinical disability in neurological as well as psychiatric diseases. Whereas previous disease decoding approaches mostly relied on expert-based extraction of features in combination with standard classification algorithms and thus strongly depend on the choice of data representation, convolutional networks are capable of learning hierarchical information directly from raw imaging data. By this, they have a great potential for finding unexpected and latent data characteristics and might perform as a real “second reader”. A major focus will be on visualization techniques to make the learned content of convolutional neural networks visible. Requirements for the PhD student: - Very good degree in computer science, mathematics, physics, psychology, computational neuroscience or related subject. - Very good programming skills (e.g. Python) - Experience in machine learning - Good writing and communication skills (in English) Please send your application (motivation+CV) in one pdf-file (in English or German) to: Dr. Kerstin Ritter Berlin Center for Advanced Neuroimaging, Bernstein-Zentrum für Computational Neuroscience Charité - Universitätsmedizin Berlin Sauerbruchweg 4, Charitéplatz 1, 10117 Berlin Tel.: + 49 30 450 539364; Email: kerstin.ritter(a)bccn-berlin.de _________________________________________________ Thank you very much! Best wishes, Kerstin Ritter _______________________________________________ Dr. rer. nat. Kerstin Ritter, nee Hackmack Bernstein Center for Computational Neuroscience Berlin Center for Advanced Neuroimaging Charité - Universitätsmedizin Berlin Sauerbruchweg 4, Charitéplatz 1, 10117 Berlin

July 20, 2017

Creating a list of important computational predictions

by Yiota Poirazi

Dear all, I believe you would agree that, the greatest recognition of our computational work comes with the experimental verification of our computational predictions. To highlight the most important outcomes of our theoretical work and facilitate a closer interaction with experimental labs so as to increase the chances of our predictions being experimentally tested, I would like to encourage you to nominate your favorite prediction at the following google form: https://docs.google.com/forms/d/e/1FAIpQLSeJZ2RrXJ0nZonIuyNzN0Cl gXDKDb7xTzoJOiqZTGxm9Kh7ow/viewform?c=0&w=1&usp=mail_form_link This effort started during the CNS 2017 meeting in Antwerp with the support of the OCNS Board. The resulting list will be posted on the CNS 2017 web site and disseminated in social media, as a reference for experimentalists. Thank you very much for supporting this important effort! Best wishes, Yiota Poirazi -- Panayiota Poirazi, Ph.D. Research Director Computational Biology Laboratory Institute of Molecular Biology and Biotechnology (IMBB) Foundation of Research and Technology-Hellas (FORTH) Vassilika Vouton, P.O.Box 1385, GR 70013, Heraklion, Crete GREECE Tel: +30 2810 391139 Fax: +30 2810 391101 Εmail: poirazi(a)imbb.forth.gr Lab site: www.dendrites.gr FENS-Kavli Network of Excellence <http://www.fens.org/Outreach/FENS-Kavli-Network-of-Excellence/> -- This message has been scanned for viruses and dangerous content by *E.F.A. Project* <http://www.efa-project.org>, and is believed to be clean. Click here to report this message as spam. <http://mailgate1.imbb.forth.gr/cgi-bin/learn-msg.cgi?id=4BCD7A00A1.A57D7&to…> -- Panayiota Poirazi, Ph.D. Research Director Computational Biology Laboratory Institute of Molecular Biology and Biotechnology (IMBB) Foundation of Research and Technology-Hellas (FORTH) Vassilika Vouton, P.O.Box 1385, GR 70013, Heraklion, Crete GREECE Tel: +30 2810 391139 Fax: +30 2810 391101 Εmail: poirazi(a)imbb.forth.gr Lab site: www.dendrites.gr FENS-Kavli Network of Excellence <http://www.fens.org/Outreach/FENS-Kavli-Network-of-Excellence/>

July 20, 2017

2nd Announcement: Computational Neuroscience in Africa: isiCN IMBIZO 18

by Tim Vogels

Dear all, we would like to draw your attention to the IBRO SIMONS COMPUTATIONAL NEUROSCIENCE IMBIZO #isiCNI2018 Get to know (and help to build) African Computational and Theoretical Neuroscience. from 7 - 28 January 2018, Muizenberg Beach, Cape Town, South Africa http://isicni.gatsby.ucl.ac.uk <http://isicni.gatsby.ucl.ac.uk/> Application deadline: 15th August 2017 The #isiCNI2018 is a southern hemisphere summer school aiming to promote computational neuroscience in Africa. It will bring together international and local students under the tutelage of the world's leading experts in the field. Like its international sister courses, this three-week summer school aims to teach central ideas, methods, and practices of modern computational neuroscience through a combination of lectures and hands-on project work. Mornings will be devoted to lectures on topics across the breadth of experimental and computational neuroscience. The rest of the day will be spent working on research projects under the close supervision of expert tutors and faculty. Individual research projects will focus on the modelling of neurons, neural systems, behaviour, the analysis of state-of-the-art neural data, and the development of theories to explain experimental observations. Who should apply? This course is aimed at Masters and PhD level students though Honours or Postdoctoral students may also apply. Students should sufficient quantitative skills, (e.g. a background in mathematics, physics, computer science, statistics, engineering or related field). Some knowledge of neural biology will be useful but not essential. Experimental neuroscience students are encouraged to apply, but should ensure that they have a reasonable level of quantitative proficiency (i.e. at least second-year level mathematics or statistics and have done at least one course in computer programming). Please distribute this information as widely as you can. Essential details * Fee (which covers tuition, lodging, and meals): 1100 EUR * Generous scholarships and travel stipends are available based on merit and need * Application deadline: 15th August 2017 * Notification of results: End of September 2017 Information and application http://isicni.gatsby.ucl.ac.uk <http://isicni.gatsby.ucl.ac.uk/> Application form http://tinyurl.com/yc6zbvpo <http://tinyurl.com/yc6zbvpo> Questions? isicn.imbizo(a)gmail.com <mailto:isicn.imbizo@gmail.com> What is an Imbizo? \ɪmˈbiːzɒ\ | Xhosa - Zulu A gathering of the people to share knowledge. FACULTY Larry Abbott - Columbia University Adrienne Fairhall - Washington University Surya Ganguli* - Stanford University Peter Latham - University College London Blake Richards - University of Toronto Timothy Lillicrap - Google DeepMind Mate Lengyel - University of CambridgeJoseph Raimondo - University of Cape Town Yiota Poirazi - Foundation for Research and Technology - Hellas Srikanth Ramaswamy - EPFL Lausanne Tim Vogels - University of Oxford Byron Yu - Carnegie Mellon University Alex Antrobus (Gatsby Unit, UCL) Athanasia Papoutsi (Foundation for Research and Technology - Hellas) William Podladski (University of Oxford ) Friedemann Zenke (Stanford University / University of Oxford) and others, to be announced *not confirmed DIRECTORS Peter Latham (Gatsby Unit for Computational Neuroscience, UCL, UK) Joseph Raimondo (University of Cape Town, South Africa) Tim Vogels (University of Oxford, UK) Sponsors The isiCNI is made possible by the generous support from the Simons Foundation (https://www.simonsfoundation.org <https://www.simonsfoundation.org/>) and IBRO, the International Brain Research Organisation (http://ibro.info <http://ibro.info/>) Organizational Affiliates University of Cape Town, University College London, University of Oxford, TReND in Africa <http://trendinafrica.org/>, CNCB <http://www.cncb.ox.ac.uk/>, Gatsby Foundation <http://www.gatsby.org.uk/>, IBRO African Center for Advanced Training in Neurosciences at UCT

July 19, 2017

Aspects of Neuroscience - Hackathon: Call for proposals (01.08) - Warsaw, 18-19th November

by Daniel Borek

On the weekend of 18-19th November, the first edition of Aspects of Neuroscience - Hackathon will take place. During this two-day event dedicated to students and PhD students, we will work in teams on neuroscience-related projects. The aim of the event is to meet new, enthusiastic researchers, to share the knowledge on data mining and brain research, but also to share the data and promote open science. We provide with a list of proposed open-access datasets, but we also encourage participants to share their own data during the event. At the moment, we opened the call for project proposals. The proposals can include various forms of a group activity, e.g., data analysis, app development, a discussion club on a particular topic, developing a software etc. Each proposal should indicate: [1] a title and abstract for the project; [2] a list of 1-5 key papers summarising the subject (which the participants should become familiar with before starting the project); [3] a list of requirements for taking part in the project (education level / English level / programming language required); [4] a maximum number of participants [5] a name of an author of the project, and a name of a senior researcher which will supervise the project during the Hackathon [6] what can the participant gain from the project? [7] an information on whether or not there is a plan for extending this work to a paper in case the results are promising An exemplary proposal is in link https://www.dropbox.com/s/ojui2h0wcz82mgy/EXEMPLARYPROPOSAL.pdf?dl=0 Location: University of Warsaw (Further information will be provided soon) Deadline for project proposals: 01.08.2017 Announcement of projects: 15.08.2017 Deadline for registration of participants: 01.11.2017 Please send your proposals to the conference email: neuroaspects(a)uw.edu.pl Proposals will be evaluated by members of our scientific committee before 15.08.2017 Main organizers: Michał Bola, PhD (Laboratory of Brain Imaging, Nencki Institute of Experimental Biology PAS, Warsaw, Poland) Natalia Bielczyk, MSc (Statistical Imaging Neuroscience Research Group, Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands) Daniel Borek, MSc (Faculty of Physics, University of Warsaw, Warsaw, Poland) Beata Goźlińska (Faculty of Physics, University of Warsaw, Warsaw, Poland) LIST OF EXAMPLARY OPEN ACCESS DATASETS: [1] calcium imaging datasets: Karl Svoboda https://crcns.org/data-sets/ssc [2] fMRI + DTI: Human Connectome Project http://www. humanconnectome.org/data/ [3] gene expression open-access database: https://www.ncbi.nlm.nih.gov/geo/ + information on gene function: www.uniprot.org [4] EEG, MRI & behavioural data from N=644 children & adolescents: http://biorxiv.org/content/early/2017/06/13/149369 [5] EEG data: http://neurotycho.org/ [6] Research data supporting "Brain connectivity during propofol sedation https://www.repository.cam.ac.uk/handle/1810/252736

July 19, 2017

PhD positions on Translational Neurosciences and Neurotechnologies - IIT@UniFe

by Alessandro D'Ausilio

PHD PROGRAM in TRANSLATIONAL NEUROSCIENCES AND NEUROTECHNOLOGIES The Center for Translational Neurophysiology of Speech and Communication (CTNSC) at the Istituto Italiano di Tecnologia (IIT) is looking for up to 4 highly motivated, full-time PhD students to work in the core research areas of the Center. At the CTNSC we focus our efforts in two integrated directions. On one side we are studying how the brain builds communicative and linguistic representations. On the other side we are designing new brain interfaces, specifically conceived for human use, to record and computationally decode neural signals. The CTNSC is hosted by the Section of Physiology of the University of Ferrara, one of the oldest in Italy (founded in 1391). In terms of its size, facilities, quality and quantity of education and research, the university is a point of excellence within Italy. The PhD student will work in Ferrara, in an international and multidisciplinary team including biomedical engineers, biologists, computer scientists, psychologists and medical doctors. The PhD positions will cover the following core areas of CTNSC: A01 Improving performance and biocompatibility of electrode arrays for brain-computer interfaces A02 Functional investigation of innovative neural interfaces A03 Investigation of sensorimotor functions in animal models (NH primates and rats) A04 Machine learning applications to multimodal brain and speech signals A05 Human neurophysiology of speech and sensorimotor communication A06 Cortical recordings in human patients during awake Neurosurgery A07 Hardware and software development for innovative exploration of brain signals DEADLINE: 1st AUGUST 2017 CTNSC Info: https://www.iit.it/centers/ctnsc-unife PhD page [ITA]: http://www.unife.it/studenti/dottorato/corsi/riforma/neuroscienze How to participate to the selection [ITA/ENG]: http://www.unife.it/studenti/dottorato/modulistica/Guidaconcorso.pdf

July 19, 2017

Postdoc + 2 PhD students in limbo, SISSA, Trieste

by Alessandro Treves

A postdoc is sought to join a HFSP-funded project to study analog cortical computations in linguistic processes. A collaboration with Naama Friedmann (TAU) and Remi Monasson (ENS). Ideal candidates have a flair for (some) language, come from a background we have not thought of and seek to get to places where they have not been, at the crossroads between neuroscience, complex systems, and poetry. Two PhD students from outside Italy are sought to later join as ESRs the EU Training Network M-GATE, on hippocampal memory functions. A network of 7 institutes + 4 companies, coordinated by Francesco Battaglia (Nijmegen). Ideal candidates, who can be of any nationality but must not have spent much time in Italy in the last 3 years, enjoy analytical, mathematical and computational excursions when in search of fundamental network understanding. Deadline August 31st, 2017. Formal applications eventually needed, but please see first obsolete limbo information http://people.sissa.it/~ale/limbo.html and contact ale(a)sissa.it well in advance. -- Alessandro Treves http://people.sissa.it/~ale/limbo.html SISSA - Cognitive Neuroscience, via Bonomea 265, 34136 Trieste, Italy +39-040-3787623 Ambassador (BlaBlaCar) +39-349-2504602

July 18, 2017