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

PhD posittion in machine learning for closed-loop deep brain stimulation

by Sebastián Castaño C.

Dear mailing-list members, We are looking for a motivated student to work with us at the Brain State Decoding lab, University of Freiburg, Germany! Specifically, we have an open PhD position for investigating machine learning methods for closed-loop deep brain stimulation systems in Parkinson's disease patients. Find the full proposal under https://www.bsdlab.uni-freiburg.de/jobs/phd-position-closed-loop-control-fo… and apply to work with us! Best on behalf of the lab, Sebastian Castaño-Candamil Doctorate student Brain state decoding lab University of Freiburg E // sebastian.castano(a)blbt.uni-freiburg.de (mailto:sebastian.castano@blbt.uni-freiburg.de)

Oct. 17, 2019

CFP: FOSDEM 2020 Open Research Tools & Technologies track

by Achilleas Koutsou

This is a *Call for Proposals* for the *Open Research Tools & Technologies* devroom/track at FOSDEM 2020. Web version: https://research-fosdem.github.io/ For the first time at FOSDEM, we are organising a track for the tools and technologies being used in and developed for researchers and scientists and the unique challenges surrounding these topics. FOSDEM (Free and Open source Software Developers' European Meeting) is a non-commercial, volunteer-organised European event centred on free and open-source software development. It is aimed at developers and anyone interested in the free and open-source software movement. It aims to enable developers to meet and to promote the awareness and use of free and open-source software. More info: https://fosdem.org/2020/about/ https://en.wikipedia.org/wiki/FOSDEM The *Open Research Tools & Technologies* devroom is a track dedicated to bringing together developers of research tools with users, potential future contributors, and developers of the wider FLOSS community to discuss the unique challenges for these particular areas of software development. We aim to: - Allow knowledge-based tool developers to publicise their efforts and become aware of other FLOSS projects. - Facilitate the pooling of coding efforts on (often poorly funded) tools. - Create a network where otherwise isolated developers and research engineers can share common concerns. - Provide social recognition for people who work in fields where designing and developing tools does not produce the traditionally recognisable outcomes, e.g., research papers. We seek talks about: - New software releases of research tools or technologies. - Feedback on open technology stacks used in research contexts (e.g., scientific research, journalistic inquiry, archive creation or publication, etc.) which collect, analyse, document, visualise, and/or share data. - Tool design and implementation for specific research contexts, e.g., how to hold an algorithm accountable to social scientists, how to foster better replicability and interoperability thanks to FLOSS, how to cope with biases of a chart for a data journalist, etc. - Issues and opportunities about bridging tech culture with research environments (research labs, libraries, newsrooms, museums, etc.). Talks will be around 20-40 minutes long + 5-10 minutes Q&A, must be in English, will be video recorded by the amazing FOSDEM staff and will be available on the FOSDEM video recordings archive. *Time and place:* Saturday 1st February 2020 from 10:30 to 19:00 ULB, Brussels, Belgium *How to submit proposals* *By submitting a proposal you agree to being recorded and to have your talk made available.* *Deadline:* Sunday 1st December 2019 23:59 CET Submissions must include: - Abstract - Session type (Lecture or Lightning talk) - Session length (20-40 min, 10 min for a lightning talk) - Expected prior knowledge / intended audience - Speaker bio The following information may also be provided but is optional: - Links to code / slides / material for the talk - Links to previous talks by the speaker Submission process is managed in the Pentabarf system used by the FOSDEM conference. Apply for a talk: https://penta.fosdem.org/submission/FOSDEM20 When submitting your talk in Pentabarf, make sure to select the *Open Research Tools and Technologies Devroom* as the Track. If you already have a Pentabarf account from a previous FOSDEM event, please reuse it. Feel free to contact me directly for any questions or concerns: koutsou(a)biologie.uni-muenchen.de <koutsou(a)bio.lmu.de> *Other devrooms that might be of interest* Even if FOSDEM is not science-specific, you might be interested by many other talks. Some developer rooms (tracks) that may be relevant to the interests of this mailing list: - HPC, Big Data, and Data Science - Graph systems and algorithms - Open source design - Community *Developer room organisers* Achilleas Koutsou, G-Node, http://g-node.org https://github.com/achilleas-k Michael Sonntag, G-Node, http://g-node.org https://github.com/mpsonntag Paul Girard, Sciences Po médialab, https://medialab.sciencespo.fr/equipe/paul-girard https://github.com/paulgirard Mathieu Jacomy, Aalborg University TANT Lab, https://www.tantlab.aau.dk/ https://github.com/jacomyma

Oct. 16, 2019

Postdoctoral position on computational modelling: interfacing models with nanoarrays to drive cultured neurons

by Yiota Poirazi

1-2 Postdoctoral positions are available in the lab of Panayiota Poirazi ( www.dendrites.gr) in Crete, starting on January 1st, 2020. The positions are for 2 years, with a possibility of renewal for another 2 years. Salary is commensurate with experience. The successful applicant will work on a multi-disciplinary project funded by the FET (Future and Emerging Technologies) Open Instrument of the European Innovation Council. The NEUREKA project aims to develop a new prototype technology that can be used for drug discovery for neurological diseases. In this new hybrid technology, computational neuronal networks that simulate dysfunction will drive cultured neurons to replicate neuropathologies. A proof-of-concept will be provided for Alzheimer’s disease, using human (iPSC)-derived neurons while testing the effects of novel drug candidates. The NEUREKA partners include the University of Padua (Prof. Vassanelli), CNRS (Prof. Larrieu), the University of Milano Bicocca (Prof. Fanciulli) and Maxwell Biosystems. Pharma advisors include Roche and Cognition Therapeutics Inc. For more information please visit: http://www.dendrites.gr/en/openings-11 Applications (full CV, statement of research interest and name and contact of 2-3 referees) should be sent by e-mail to poirazi(a)imbb.forth.gr, quoting “NEUREKA: Postdoctoral position” in the subject line. The deadline for applications is *November 30th, 2019*. Applications will be examined until the position is filled. Informal enquiries are welcome. -- Panayiota Poirazi, Ph.D. Research Director 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

Oct. 16, 2019

Post-doctoral Researcher in Computational modelling of hippocampal circuits (Blue Brain Porject, Switzerland)

by Armando Romani

Blue Brain Porject (Campus Biotech, Geneva, Switzerland) is looking for a *Post-doctoral Researcher in Computational modelling of hippocampal circuits*. Improve the existing large-scale models of rodent hippocampus. The current network models are already the product of several iterations and their emergent behavior can reproduce many features of the hippocampus. The work on the models continues by expanding the region of interest from CA1 (the first region we considered) to the full hippocampus, and eventually by connecting the hippocampus to the rest of the brain. In parallel, the models will include more or more details. For example, we are working on including gap junctions, long-term plasticity, structural plasticity, neuromodulation, glia, vasculature, and so on. Exploit the models to answer outstanding questions in the field, such as information processing in the hippocampus, spatial navigation, memory processes, development of pathological conditions (Alzheimer’s disease, epilepsy). The models are designed not to answer one specific question, but for a general purpose. This ensures a larger validity of the models and allows us to potentially test many different hypotheses and make likewise predictions. Follow the link below to learn more about the position and how to apply. https://recruiting.epfl.ch/Vacancies/1005/Description/2 — Armando Romani, PhD Junior Group Leader - Simulation Neuroscience Division EPFL - Blue Brain Project Campus Biotech Chemin des Mines 9 CH-1202 Geneva, Switzerland Phone +41 (0)21 693 7190

Oct. 16, 2019

Post-doctoral Researcher in Computational modelling of thalamo-cortical circuits (Blue Brain Porject, Switzerland)

by Armando Romani

Blue Brain Porject (Campus Biotech, Geneva, Switzerland) is looking for a* Post-doctoral Researcher in Computational modelling of thalamo-cortical circuits*. The goal of this project is to leverage the Blue Brain software and existing thalamic models to build and validate biologically-accurate models of thalamo-cortical circuitry. Modelling these circuits is a crucial step to investigate brain functions, such us sensory transmission, sleep rhythms, wakefulness, alertness. The successful candidate would be responsible for gathering data about thalamo-cortical circuits from the literature, open-access datasets and in vitro studies in collaboration with the experimental lab. Interactions with biology and experimental experts would be fundamental to validate and confirm model predictions. In addition, the candidate would provide guidance and scientific expertise to the technical teams and contribute to the on-going refinement of workflows and tools to build data-driven unifying brain tissue models. Furthermore, the candidate will work in collaboration with engineering teams on visualization, high performance computing, data integration and with project managers to define objectives and timelines to achieve overarching objectives and meet aggressive deadlines. Follow the link below to learn more about the position and how to apply. https://recruiting.epfl.ch/Vacancies/827/Description/2 — Armando Romani, PhD Junior Group Leader - Simulation Neuroscience Division EPFL - Blue Brain Project Campus Biotech Chemin des Mines 9 CH-1202 Geneva, Switzerland Phone +41 (0)21 693 7190

Oct. 16, 2019

Human Neocortical Neurosolver New Features & SFN 2019 Demos

by Stephanie Jones

We are happy to announce several exciting developments with the new Human Neocortical Neurosolver (HNN) software designed for cell and circuit interpretation of human EEG/MEG. 1. An updated version of HNN with a new, frequently requested feature of parameter optimization (with a tutorial) is now available. Check it out at hnn.brown.edu. 2. HNN will be presented with live demonstrations at SFN 2019 in Chicago, IL. Sunday October 20th 11-11:30am Carney Booth 2129 Sunday October 20th 6:30-8:30pm BRAIN Initiative Alliance Tools & Technology Social Hyatt Regency McCormick Place, Ballroom CD Monday October 21th 11-11:30am Carney Booth 2129 Monday October 21st 6:45pm Open-Source Technology Social Hyatt Regency McCormick Place, Room N135 Wednesday October 23rd 1-5pm McCormick Place: Hall A. Poster 729.06 3. A HNN methods paper is now available on bioRxiv (Neymotin et al, BioRxiv 2019:740597. https://doi.org/10.1101/740597 <https://doi.org/10.1101/740597>) ******************************************* Stephanie R. Jones, PhD Associate Professor Brown University Department of Neuroscience Stephanie_Jones(a)Brown.edu https://blogs.brown.edu/joneslab/ <https://blogs.brown.edu/joneslab/> Human Neocortical Neurosolver https://hnn.brown.edu <https://hnn.brown.edu/>

Oct. 16, 2019

AREADNE 2020 Conference Announcement

by John Pezaris

AREADNE 2020 Research in Encoding and Decoding of Neural Ensembles Nomikos Conference Centre, Santorini, Greece 16-20 June 2020 http://areadne.org info(a)areadne.org The AREADNE conferences bring scientific leaders from around the world to present their recent findings on the functioning of neuronal ensembles in an informal yet spectacular setting on Santorini. The conference series emphasizes interaction with a size and pace that encourages in-depth discussion. Interested researchers are strongly encouraged to submit an abstract for poster presentation as attendance is strictly limited, and the conference typically sells out. Abstract submission deadline is 24 Jan 2020. Send us your best work!

Oct. 15, 2019

Reminder: 1st Elephant User Workshop for Reproducible Data Analysis in Electrophysiology, Paris, Nov 4-6, 2019

by Michael Denker

Reminder for the ***1st Elephant User Workshop*** --Accelerate Structured and Reproducible Data Analysis in Electrophysiology-- Paris, France Nov 4-6, 2019 Summary: In this workshop, users will be trained in the use of community-driven tools developed in the context of the Human Brain Project to analyze electrophysiological data, such as spike train data or LFP time series. In addition, participants receive help in integrating their own data into such analysis workflows. The topics covered will be: * reading and manipulating electrophysiology data in Python using Neo [1] * analysis of such data using Elephant [2] * best practices for integrating metadata into your workflow to aid the analysis process * best practices for structuring of analysis results * tracking data analysis pipelines using the HBP Knowledge Graph [3] * collaboration and sharing using the HBP Collaboratory [4] For more information and registration, check out: https://www.humanbrainproject.eu/en/education/participatecollaborate/infras… Organizers: Andrew Davison | French National Centre for Scientific Research, France Michael Denker | Forschungszentrum Jülich, Germany Martina Schmalholz | Heidelberg University, Germany References: [1] Neo, https://neo.readthedocs.io [2] Elephant, https://elephant.readthedocs.io [3] HBP Knowledge Graph, https://www.humanbrainproject.eu/en/explore-the-brain/ [4] HBP Collaboratory, https://collab.humanbrainproject.eu ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Oct. 15, 2019

Neuroimaging data scientist position in Marseille, France

by Sylvain Takerkart

Neuroimaging Data Scientist Multimodal neuroimaging study of cerebellar anomalies in Parkinson’s disease The project SENCE (Movement disorders in Parkinson’s disease: The role of somatosensory deficits and cerebellar anomalies) is funded by the French National Research Agency (ANR) and conducted in collaboration with the University of Oxford (Medical Research Council - MRC). It investigates the anatomical anomalies and abnormal metabolism of the cerebellum resulting from basal ganglia deregulation in Parkinson’s Disease (PD), which may contribute substantially to motor deficits. To this aim, we collect in PD patients (and healthy controls) an original multimodal neuroimaging dataset, comprising anatomical, diffusion-weighted (DWI), and resting state fMRI (rs-fMRI), as well as FDG-PET images, complemented by behavioural and electrophysiological recordings (EEG/intracranial LFP) collected in the same participants during motor tasks performed ON/OFF dopaminergic medication and/or ON/OFF deep brain stimulation (using open- or closed-loop adaptive stimulation protocols). -- Missions -- The data scientist will be responsible to set-up processing pipelines dedicated to analyzing the different neuroimaging scan types (MRI and PET), both at the full-brain level and with a particular focus on the characterization of the anatomy, connectivity and metabolism of the cerebellum. These neuroimaging results will also be combined with behavioural and electrophysiological data which will be analysed by other members of the project team. Furthermore, the data scientist will organize the raw and processed data in a standardized fashion to make it accessible to all the consortium and to the scientific community at large. These missions fall into our commitment to reproducible science through open code and data. -- Profile -- This position is for a candidate who is comfortable (or proficient) with computer programming (python will be our language of choice; matlab will also be used) and has good knowledge and/or experience in signal and image processing. It can be of interest to different types of profiles. You are a young graduate (BSc or MSc) either in data science, in electrical engineering or in neuroscience and you want to be at the heart of an innovative medical imaging project, with the possibility to continue as a PhD student. Or you already have a PhD in a relevant field and you want to take this opportunity to fulfill the aforementioned missions while getting further involved in the research aspects of the project, which should offer excellent opportunities for publications in neuroscience or methodological journals. -- Working environment -- The Institut de Neurosciences de la Timone (INT) is one of the top French neuroscience research institutes with 150 staff members gathered in 10 inter-disciplinary teams examining different aspects of the cerebral organization. It is located on the medical campus of Aix-Marseille University. The successful candidate will join the SENCE project’s team within INT and will interact with cognitive neuroscientists, theoretical neuroscientists as well as specialists in neuroimaging data acquisition and processing. Marseille, the second largest city in France, is a vibrant inter-cultural hub located on the Mediterranean shore, and only 2h away from the Alps mountains. The position is initially open for one year, with a possible renewal for two more years. Starting date can be as early as December 2019 and can be postponed until the position is fulfilled. If you are interested, please send your resume and cover letter to: Sylvain_DOT_Takerkart_AT_univ-amu_DOT_fr and Nicole_DOT_Malfait_AT_univ-amu_DOT_fr -- Sylvain Takerkart Institut des Neurosciences de la Timone (INT) UMR 7289 CNRS-AMU Marseille, France tél: +33 (0)4 91 324 007 http://www.int.univ-amu.fr/_TAKERKART-Sylvain_?lang=en

Oct. 15, 2019

ANDA 2020 - G-Node Advanced Neural Data Analysis Course, April 14-30, 2020, Jülich, Germany

by Thomas Wachtler

ANDA 2020 - G-NODE ADVANCED NEURAL DATA ANALYSIS COURSE April 14 - 30, 2020 Haus Overbach, Jülich-Barmen, Germany Techniques to record neuronal data from populations of neurons are rapidly improving. Simultaneous recordings from hundreds of channels are possible while animals perform complex behavioral tasks. The analysis of such massive and complex data becomes increasingly challenging. This advanced course aims at providing deeper training in state-of-the-art analysis approaches in systems neuroscience. The course is addressed to excellent master and PhD students and young researchers who are interested in learning advanced techniques in data analytics and in getting hands-on experience in the analysis of electrophysiological data. Internationally renowned researchers will give lectures on statistical data analysis and data mining methods with accompanying exercises. Students will define and perform their own analyses on provided data to solve a challenge. Participants are required to have a strong interest in data analysis, a background in a mathematical or related field, knowledge of algebra, matrix operations, and statistics, and need to have solid programming experience (preferably in Python). FACULTY · Moshe Abeles, Hebrew Univ. Jerusalem, Israel · Michael Denker, Jülich Research Center, Germany · Udo Ernst, Univ. Bremen, Germany · Sonja Grün, Jülich Research Center, Germany · Adam Kohn, Albert Einstein College of Medicine, New York, USA · Jakob Macke, TU Munich, Germany · Luca Mazzucato, Univ. of Oregon, Eugene, USA · Martin Nawrot, Univ. of Cologne, Germany · Yifat Prut, Hebrew Univ. Jerusalem, Israel · Hansjörg Scherberger, German Primate Center, Göttingen, Germany · Thomas Wachtler, LMU Munich, Germany TOPICS COVERED Single neuron properties and statistics · Stochastic processes · Surrogate methods · Detection of spatio-temporal patterns · Unitary Events · Statistical analysis of massively parallel spike data · Higher-order correlation analyses · Elephant toolbox · Spike-LFP relationship · Population coding · State space analysis · Machine learning · Data mining · Research data management and reproducibility REQUIREMENTS Applicants should be familiar with linear algebra, probability, differential and integral calculus and experienced using Python or Matlab. Preparatory reading material will be provided. Students should bring their own laptops and should be able to install software on their system. Students that do not have a suitable laptop should indicate this immediately after acceptance to the course. We will be able to provide a small number of laptops for the time of the course. COURSE FEE A course fee of 1000 Euros will be charged to cover costs for accommodation and meals. Limited financial support may be available for students that otherwise would not be able to attend, which is to be indicated in the application. HOUSING Accommodation in 2-bed rooms for students will be provided at the course site. HOW TO APPLY The application should include · a letter of motivation (max 1 page) · curriculum vitae (please indicate the relevant courses you have taken) · description of programming experience · a letter of recommendation. Please send all documents as a single PDF file to <advanced-course(a)g-node.org>. APPLICATION DEADLINE Applications must be received by NOVEMBER 15, 2019. Early application is encouraged. For further information see http://www.g-node.org/anda

Oct. 15, 2019