February 2019 - Comp-neuro - lists.cnsorg.org

Prometheus: Cloud Computing Portal for Computational Optogenetics

by Nikolic, Konstantin

We would like to announce the availability of "Prometheus: Cloud Computing Portal for Computational Optogenetics". This is a web-based portal for PyRhO - a set of tools with a GUI for modelling and simulating opsins in neurons, using Python, Neuron or Brian 2. The main attraction is that all necessary modules and dependencies are already installed and configured (including the Python programming language, commonly used scientific Python libraries, NEURON and Brian2 simulation platforms) and the GUI comes with some pre-loaded values. So the platform can be used immediately. Absolutely no installation or set-up is required, just a web-browser, since the portal is using IPython/Jupyter<https://jupyter.org/> notebook. The portal is available here: http://try.projectpyrho.org/ To simplify things, there is no registration wall at the moment. But please note that the resources we are currently renting from a cloud computing service provider are limited. So please be patient - sometimes it might take more time to execute your job, depending on the number of users running their codes at the same time. A paper describing the platform, including several demonstrations, has been published: Evans et.al: "PyRhO: A Multiscale Optogenetics Simulation Platform", Frontiers in Neuroinformatics (2016): https://www.frontiersin.org/articles/10.3389/fninf.2016.00008/full Best regards, Dr Benjamin Evans, Bristol University, UK Dr Konstantin Nikolic, Imperial College London, UK

Feb. 11, 2019

MBL Methods in Computational Neuroscience Course

by Stephen A. Baccus

Applications are open for the Methods in Computational Neuroscience course at the Marine Biology Laboratory in Woods Hole, MA. The course will run from July 29 to August 23, 2019, and the online application form can be found at: https://ws2.mbl.edu/studentapp/studentapp.asp?courseid=MCN The course application deadline is *March 19*. The course covers a range of topics in computational neuroscience including neuronal biophysics, neural coding & information processing, circuit dynamics, learning & memory, motor control, and cognitive processing & disease. In addition, numerous tutorials and problem sets will cover a broad range of computational and mathematical modeling methods. The course strongly emphasizes the collaboration between theory and experiment in solving neuroscience problems, and lectures will be given by a mixture of theorists and experimentalists. The final weeks of the course are primarily reserved for work on projects that students design in collaboration with the resident faculty. Further information can be found on the MCN website: http://www.mbl.edu/mcn/ 2019 Course Directors: Stephen Baccus, Stanford University Xiao-Jing Wang, New York University 2019 Confirmed Faculty: Larry Abbott, Columbia University Emery Brown, MIT Dmitri Chklovskii, Simons Institute Anne Collins, UC Berkeley Shaul Druckmann, Stanford University Uri Eden, Boston University Bard Ermentrout, U. of Pittsburgh Adrienne Fairhall, U. of Washington Ila Fiete, University of Texas Austin James Fitzgerald, Janelia Res., HHMI Loren Frank, UCSF Michale Fee, MIT Stefano Fusi, Columbia University Surya Ganguli, Stanford University Mark Goldman, UC Davis Kenneth Harris, U. College London James Haxby, Dartmouth University Nancy Kopell, Boston University Eve Marder, Brandeis University Bartlett Mel, Univ. of Southern California Jonathan Pillow, Princeton University David Redish, U. Minnesota Terry Sejnowski, Salk Institute Mike Shadlen, Columbia U. Reza Shadmehr, Johns Hopkins Univ. Sara Solla, Northwestern University Haim Sompolinsky, Hebrew University Klaas Stephan, Univ. of Zurich Josh Tenenbaum, MIT Nao Uchida, Harvard University Greg Wayne, DeepMind Hongkui Zeng, Allen Institute

Feb. 9, 2019

Postdoctoral Fellow in Multimodal Brain Imaging of Neurodegeneration

by Yasser Iturria Medina

*Postdoctoral Fellow in Multimodal Brain Imaging of Amyotrophic Lateral Sclerosis (ALS)* We are looking for a highly motivated postdoctoral student, for joining the *Neuroinformatics for Personalized Medicine* lab (NeuroPM) at the Montreal Neurological Institute (McGill University, Montreal, Canada). The postdoc will be under the supervision of Professors Yasser Iturria-Medina (McGill University) and Sanjay Kalra (University of Alberta), and will be expected to collaborate with multiple associated groups. The project, for one year and potentially extendable for another year, includes the analysis of direct multifactorial brain interactions and intra-brain network spreading of aberrant effects in Amyotrophic Lateral Sclerosis. The NeuroPM lab (*http://www.neuropm-lab.com/ <http://www.neuropm-lab.com/>*) is affiliated with the Healthy brain for Healthy Lives (HBHL) initiative (*https://www.mcgill.ca/hbhl/ <https://www.mcgill.ca/hbhl/>*), the Ludmer Center (*http://ludmercentre.ca/ <http://ludmercentre.ca/>*), and the McConnell Brain Imaging Center ( https://www.mcgill.ca/bic/) involving computationally intensive and interdisciplinary research on the brain. The MNI is an internationally renowned institution, characterized by the integration of research and patient care. The Kalra Lab (http://www.ualberta.ca/ALS/research/) has the mission of improving our understanding of ALS biology through brain imaging and translational research. It is the central coordinating site for the Canadian ALS Neuroimaging Consortium (CALSNIC), a multicenter research platform for the collection of harmonized imaging and behavioural data. Interested candidates should have a background in brain imaging and Matlab. Experience in neurodegeneration and brain computational analysis will be an asset. Interested persons should send their CV, a cover letter stating research interests, and two reference letters. The competition will remain open until the position is filled. *Contact*: Yasser Iturria Medina, Email: iturria.medina(a)gmail.com -- Yasser Iturria Medina, PhD. Montreal Neurological Institute, McGill University Montreal, Canada H3A 2B4, Phone # 514-398-1524 Lab: http://www.neuropm-lab.com/

Feb. 9, 2019

PhD positions - Learning in Spiking Neural Networks

by Robert Legenstein

The Lab of Robert Legenstein at TU Graz is offering funded PhD positions in the areas Spiking Neural Networks/Machine Learning/Brain Models/Neuromorphic Hardware. A background in Machine Learning, Computer Science, or Mathematics is desirable, as well as evidence for excellent prior performance as a student. Successful candidates will work on learning algorithms for spiking neural networks in the interdisciplinary consortium of the EU-funded project SYNCH. We will develop in this project learning algorithms for spiking neural networks (unsupervised, supervised, and reward-based). Hardware experts will implement these algorithms in cooperation with our team in a spiking neural network chip. The chip will be applied to various tasks within a brain-silicon hybrid system such as the classification of recorded brain network states. (see https://www.tugraz.at/institute/igi/people/prof-legenstein/projects/ for a brief description). Please send your application including a CV, any prior thesis and/or work by February 28 to robert.legenstein(a)igi.tugraz.at Dr. Robert Legenstein Institute Head Institute for Theoretical Computer Science Graz University of Technology Inffeldgasse 16b/I, 8010 Graz, Austria http://www.igi.tugraz.at/legi/ Follow @CompLegenstein on Twitter. ++43/316/873-5824 ----------------------------------

Feb. 8, 2019

Postdoctoral position in network modeling

by Fidel Santamaria

Postdoctoral position in network modeling An NIH-funded postdoctoral position is available in the lab of Charles Wilson at the Neurosciences Institute of the University of Texas at San Antonio, on the topic of oscillations and oscillatory coupling in the basal ganglia. The successful applicant will join a team of experimentalists to create a large scale accurate model of the basal ganglia, with a focus on activity pattern formation by oscillating neurons in the globus pallidus, subthalamic nucleus and substantia nigra. Applicants should have an interest in the function of the basal ganglia and experience making and using models of neurons and networks. Experience with intracellular recoding is beneficial, but not required. For information about the lab see: https://marlin.life.utsa.edu/ For information about the UTSA Neurosciences Institute see: https://neuroscience.utsa.edu/ To apply please send your CV, a letter describing your experimental interests and contact information for two potential references to Charles Wilson (charles.wilson(a)utsa.edu<mailto:charles.wilson@utsa.edu>).

Feb. 8, 2019

Post-doc position neuropysiology of hearing impairment and machine learning

by Jochem Rieger

Dear list, The DFG-funded cluster of Excellence "Hearing 4 All" has an open post-doctoral position in project "Characterizing central neural speech processing in normal and hearing impaired listeners using machine learning". The aim of the project is to combine neurophysiological measurements (fMRI and/or MEG/EEG) with data driven machine learning to characterize cortical consequences of hearing loss. We offer an international and interdisciplinary research environment and access to up-to-date research facilities. The position is available from April 1st, 2019 until October 31st, 2022. Salary level German TV-L E13, full time. The payment includes an experience dependent component. Application deadline is February 27th 2019 The full job announcement can be found here: https://uol.de/stellen/?stelle=66447 Please forward this message to people who might be interested Regards, Jochem -- Prof. Dr. rer. nat. Jochem Rieger Head of Applied Neurocognitive Psychology Head of Neuroimaging Unit Faculty VI Carl-von-Ossietzky University 26111 Oldenburg Germany Phone: +49(0)4417984533 Fax: +49(0)4417983865

Feb. 8, 2019

Brainhack Warsaw (March 1–3, 2019, Poland)

by Daniel Borek

Brainhack Warsaw 2019 March 1-3, 2019 University of Warsaw, Warsaw, Poland — REGULAR -> 04.02 - 17.02 -> 120 PLN (ABOUT €29) — — LATE -> 18.02 - 24.02 -> 135 PLN (ABOUT €33) — On the weekend of March 1-3, 2019, the second edition of Brainhack Warsaw will take place. During this three-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, make new friendships in academia, learn, share the knowledge on data mining and brain research, but also promote open science in the spirit of the whole Brainhack community (Craddock et al., 2016) <https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0121-x>. Attendees of various backgrounds are welcome to join! Below you could see a list of projects which will be realised during our three-day event: - Generating fake MRI to enhance Alzheimer’s disease prediction <https://brainhackwarsaw.github.io/index.html#project2> - Network analysis of the electrical activity of the brain during epileptic seizures <https://brainhackwarsaw.github.io/index.html#project3> - Deep Frankenstein: dissecting and sewing artificial neural networks <https://brainhackwarsaw.github.io/index.html#project4> - Tackling the ABCD Neurocognitive Prediction Challenge <https://brainhackwarsaw.github.io/index.html#project5> - Multidimensionality problem in passive BCI for game control <https://brainhackwarsaw.github.io/index.html#project6> - Cross-Recurrence Quantification Analysis (cRQA) as a new measure of functional connectivity <https://brainhackwarsaw.github.io/index.html#project7> - EMG-based desktop controlling <https://brainhackwarsaw.github.io/index.html#project8> - Mapping the state of modern psychology through the public online activity of scientists <https://brainhackwarsaw.github.io/index.html#project9> ‘Regular’ and ‘Late’ registration for project participants close subsequently on 17.02 and 24.02.2019. A registration fee will be requested after registration. The registration fee will be spent on catering during the event. To register please visit our page and learn more about the Brainhack Warsaw! https://brainhackwarsaw.github.io/ We looking forward to seeing you in Warsaw! On behalf of the Brainhack Warsaw 2019 team

Feb. 8, 2019

Computational & Cognitive Neuroscience Summer School 2019

by Christopher Honey

We are pleased to announce the 9th Computational and Cognitive Neuroscience (CCN) Summer School which will take place June 29 - July 21, 2019 in Suzhou, China. Designed to emphasize higher cognitive functions and their underlying neural circuit mechanisms, the course aims at training talented and highly motivated students and postdoctoral fellows from Asia and around the world. We welcome both applicants with quantitative backgrounds (including Physics, Mathematics, Engineering and Computer Science) and those with experimental backgrounds. The lectures will introduce the basic concepts and methods, as well as cutting-edge research on higher brain functions such as decision-making, attention, learning and memory. Modeling will be taught at multiple levels, ranging from single neuron computation and microcircuits up to large-scale systems and machine-learning approaches. Python-based programming labs coordinated with the lectures will provide practical training in important computational methods. Course information and application instructions are available on the CCN Summer School website: www.ccnss.org Applications are being accepted through the Cold Spring Harbor Asia website: http://www.csh-asia.org/summerschool_SCOSYNEinstruct.html The application deadline is March 8, 2019. Faculty: Carlos Brody (Princeton) Bob Desimone (MIT) Bard Ermentrout (Pitt) Winrich Freiwald (Rockefeller) Biyu He (NYU) Sukbin Lim (NYU) John Murray (Yale) Jascha Sohl-Dickstein (Google Brain) Jon Winawer (NYU) Byron Yu (CMU) Organizers: Dora Angelaki (NYU) Xiao-Jing Wang (NYU) Christopher Honey (Johns Hopkins) Robert Guangyu Yang (Columbia) Feel free to direct any questions to Chris Honey ( chris.honey(a)jhu.edu ) and Robert Guangyu Yang ( robert.yang(a)columbia.edu ).

Feb. 8, 2019

PhD position in DFG project: Active vision: control of eye-movements and probabilistic planning @TU Darmstadt

by Constantin Rothkopf

Applications are invited for a PhD student position in the lab of Constantin Rothkopf at the Technical University Darmstadt. The position is initially funded by the German Research Foundation DFG for three years. The project 'Active vision: control of eye-movements and probabilistic planning' aims to investigate how humans carry out eye-movements across different tasks and how this can be understood with models of probabilistic planning. Recent publications of the lab on this topic include the following papers: - Hoppe, D., & Rothkopf, C. A. (2016). Learning rational temporal eye movement strategies. Proceedings of the National Academy of Sciences, 113(29), 8332-8337. - Hoppe, D., & Rothkopf, C. A. (2019). Multi-step planning of eye movements in visual search. Scientific reports, 9(1), 144. Applicants need to have a Masters degree in cognitive science, computer science, psychology, or related fields. In addition to a strong general interest in cognitive science, computational science, experimental psychology, and interdisciplinary research, the ideal candidate has a background in eye-tracking and probabilistic planning. Analytical know-how, awareness of experimental literature, and experience with programming (e.g. Python, Matlab, C++) are indispensable. We offer a supportive and multidisciplinary environment driven by scientific curiosity, lab facilities for measuring eye and body movements in extended behavior in-the-wild and in VR, and collaborations with universities and research institutes in Frankfurt, Giessen, as well as internationally. The lab is part of the Centre for Cognitive Science and the Institute of Psychology at TU Darmstadt. If you are interested, please send a CV, a brief (max. 2 pages) cover letter explaining your research interests, what you are looking for in a PhD, why you would like to study in the lab, your longer term career goals, and the names and contact details of 2-3 academic references to constantin.rothkopf(a)cogsci.tu-darmstadt.de until February 28th 2019, but later applications will be considered until the position is filled. -- Constantin A. Rothkopf, PhD http://www.pip.tu-darmstadt.de/ http://www.cogsci.tu-darmstadt.de/ http://www.ai-da.tu-darmstadt.de/

Feb. 7, 2019

FENS SfN Summer School 2019 on brain reading and writing: new perspectives of neurotechnology - apply by 18 February

by FENS Schools

Dear Colleagues, This year's FENS-SfN neuroscience summer school on *Brain reading and writing: new perspectives of neurotechnology* will take place on 2-8 June in Bertinoro, Italy. We would like to invite you to have a look at the programme below. *Scientific chairs*: *Dr. Pieter Roelfsema* <https://nin.nl/research/researchgroups/roelfsema-group/>, Netherlands Institute for Neuroscience, The Netherlands *Dr. Andrew B. Schwartz* <http://motorlab.neurobio.pitt.edu/schwartz.php>, Department of Neurobiology, School of Medicine, University of Pittsburgh, USA *School Programme Description* During this school, we will discuss the intracortical methods being developed for reading from, and writing to, the brain. A set of international lectures will provide an overview of the emerging therapeutic applications made possible with this technology. In addition to being exposed to new hardware, students will learn about, and apply new computational approaches to facilitate brain-device communication. We will discuss some of the interesting ethical ramifications of a neuro-technologically assisted future. *Faculty members*: *Matteo Carandini* <https://www.carandinilab.net/>, Cortexlab, UCL, UK *Xinyan Tracy Cui* <https://www.engineering.pitt.edu/cui/>, Department of Bioengineering, University of Pittsburgh, USA *Eduardo Fernandez* <https://www.umh.es/contenido/pdi/:persona_4122/datos_en.html>, Institute of Bioengineering, Universidad Miguel Hernández de Elche, Spain *Tim Harris* <https://www.janelia.org/lab/harris-lab>, Howard Hughes Medical Institute, Janelia Research Campus, USA *Karin Jongsma* <https://www.umcutrecht.nl/en/Research/Researchers/Jongsma-Karin-KR>, Julius Center, University Medical Center Utrecht, The Netherlands *Jason Kerr* <https://www.caesar.de/en/our-research/behavior-and-brain-organization/direc…>, Department of Behavior and Brain Organization, Research Center caesar, Bonn, Germany *Stephanie Lacour* <https://cnp.epfl.ch/Lacourlab>, Center for Neuroprosthetics, EPFL, Switzerland *Antonio Regalado* <https://www.technologyreview.com/profile/antonio-regalado/>, MIT Technology Review, USA *José-Alain Sahel* <http://www.mirm.pitt.edu/our-people/faculty-staff-bios/jose-alain-sahel-md/>, Department of Ophthalmology, University of Pittsburgh School of Medicine, USA *Eilon Vaadia* <https://elsc.huji.ac.il/index.php?q=vaadia/home>, Edmond and Lily Safra Center for Brain Sciences, Israel *Anna Wang Roe* <http://www.ziint.zju.edu.cn/index.php/Index/index.html>, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology (ZIINT), China *Byron Yu* <https://users.ece.cmu.edu/~byronyu/>, Electrical & Computer Engineering and Biomedical Engineering, Carnegie Mellon University, USA *Application form*: http://www.fens.org/Training/FENS-Schools/Summer-School-2019/Application-Fo… *Deadline*: 18 February 2019, 3pm CET. Further information about the school and available stipends can be found here <https://www.fens.org/Training/FENS-Schools/Summer-School-2019/>. Feel free to share this enriching opportunity with your professional network. Best regards, FENS Schools Administration

Feb. 7, 2019