- Comp-neuro - lists.cnsorg.org

Reminder: 1st Elephant User Workshop for Reproducible Data Analysis in Electrophysiology, Paris, Nov 4-6, 2019
by Michael Denker Oct. 15, 2019

Oct. 15, 2019

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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Neuroimaging data scientist position in Marseille, France
by Sylvain Takerkart Oct. 15, 2019

Oct. 15, 2019

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

1 0

Open-Rank Position: Bilkent University
by Hulusi Kafaligonul Oct. 14, 2019

Oct. 14, 2019

*Open-Rank Position, Aysel Sabuncu Brain Research Center and National Magnetic Resonance Research Center (UMRAM) at Bilkent University* Bilkent University invites faculty applications (rank open) for a position in the Aysel Sabuncu Brain Research Center and National Magnetic Resonance Research Center (UMRAM). The strategic plan includes an expansion of research related to molecular and cellular neuroscience. Accordingly, we seek applications from promising or established scholars who have worked in this or a related field, and who integrates or plans to integrate neuroimaging in their studies. The newly built research center has spacious state-of-the-art molecular and cellular laboratories, in addition to animal research facilities. An Interdisciplinary Graduate Program in Neuroscience offers Master's and PhD programs that was opened five years ago. Finally, there are also human psychophysics, EEG laboratories and two MRI scanners (3T and 1.5T) with plans to purchase a high field scanner (7T) for animal studies. Bilkent is located in Ankara, Turkey's metropolitan capital with daily direct flights to Istanbul and other major European cities. Bilkent University also provides faculty members and their families with free housing and access to private health insurance. Qualifications and Responsibilities: Applicants should have a PhD in neuroscience or related discipline, and should have an excellent publication record (requirements vary with rank). A demonstrated ability or the potential to secure external research funding will be a strong advantage. Faculty members are expected to maintain productive research programs. Successful applicants will teach during the Fall and Spring semesters with no teaching requirement during summer, and supervise PhD and Master's students. Appointment: This full-time appointment will begin in September 2020 (negotiable). Salary will be internationally competitive and commensurate with qualifications and experience. *Application Procedure* Applicants should submit 1. a cover letter; 2. CV; 3. research statement; 4. teaching statement; 5. pdf copies of 3 representative publications; and 6. contact information for 3-5 professional references. Review of applications will commence on November 30, 2019 and continue until the position is filled. Inquiries about the university should be directed to Hulusi Kafaligonul athulusi(a)bilkent.edu.tr <mailto:hulusi@bilkent.edu.tr>or +90 312 290 3016.To apply please go to the following link: https://stars.bilkent.edu.tr/staffapp/UMRAM2019For more information, please visit the following websites: beyin.bilkent.edu.tr <http://beyin.bilkent.edu.tr/> umram.bilkent.edu.tr <http://umram.bilkent.edu.tr/> neuro.bilkent.edu.tr <http://neuro.bilkent.edu.tr/> bilkent.edu.tr <http://bilkent.edu.tr/> -- Hulusi Kafaligonul Assistant Professor National Magnetic Resonance Research Center Interdisciplinary Neuroscience Program Bilkent University, Ankara, Turkey http://hulusi.bilkent.edu.tr/ -- Bu e-posta virüslere karşı Avast antivirüs yazılımı tarafından kontrol edilmiştir. https://www.avast.com/antivirus

1 0

PhD and Postdoc positions in Frankfurt, Germany
by Martin Vinck Oct. 12, 2019

Oct. 12, 2019

Apologies for cross-posting: The laboratory of Dr. Martin Vinck at the Ernst Struengmann Institute for Neuroscience in Cooperation with Max Planck Society <http://www.esi-frankfurt.de/esi-frankfurt/>is seeking multiple Postdocs and PhDs for experimental projects in marmoset (ideally starting early spring of 2019). We will study predictive processing in the visual system, test new models of object recognition, and the contribution of different cell types to neural coding. Data will be collected with chronic, high-density silicon probes including wireless recordings during (freely moving) natural behavior (using the eCube white matter system). A part of the project involves optogenetics. Additional training in high-density electrophysiology can be acquired by participation in projects in mice. You will work closely together with computational scientists in our laboratory working on deep learning and state space analyses. The main focus of the project is the interpretation of neural activity from artificial neural networks (in particular recurrent and predictive neural networks) and the study of population coding. We are looking for candidates with a biology or medicine background and experience in behavioral training and electrophysiology. Frankfurt is an internationally oriented city with many neuroscience institutes in the neighbourhood, e.g. the Max Planck Institute for Brain Research <http://brain.mpg.de/home.html>, the FIAS <https://fias.institute/>, the Interdisciplinary Center for Neuroscience <https://www.izn-frankfurt.de/en/>, and the institute for Empirical Aesthetics. Interested candidates are invited to send their application materials in electronic form (PDF format) to martin.vinck(a)esi-frankfurt.de. The first deadline for applications is 7 of November 2019. Applications should contain a letter of intent, a detailed curriculum vitae, lists of university courses completed with marks obtained, and the names of at least two scientists who can give references (or at least two reference letters). The advertisement will be valid until positions are filled. Positions are not yet filled.

1 0

PhD studentship in Bristol
by Cian O'Donnell Oct. 12, 2019

Oct. 12, 2019

We are looking for a computational neuroscience PhD student to start September 2020 to do computational modelling of synaptic plasticity in neurodevelopmental brain disorders. You would mainly be based in the University of Bristol in the group of Cian O’Donnell, and co-supervised by Krasi Tsaneva-Atanasova (University of Exeter) and Jeremy Hall (Cardiff University). Your background can be flexible but training in neuroscience, mathematical modelling and/or scientific programming would be beneficial. Usually we use Julia, Python or Matlab programming languages. Project outline: Autism and Schizophrenia, two of the most common neurodevelopmental disorders, have been linked with ~100 different genetic mutations each. Many of the implicated genes code for proteins involved in synaptic plasticity. It may be that these distinct mutations converge to give similar alterations to the “rules of synaptic plasticity”, and therefore affect learning and development. L-type calcium channel are one notable example, frequently popping up in risk gene lists and known to play crucial roles in synaptic plasticity. In this PhD project you would extend our existing biophysical models of calcium signalling at rodent hippocampal synapses to try to figure out the role of dysfunctional L-type calcium ion channels in these brain disorders. A more detailed project description can be found here: https://www.gw4biomed.ac.uk/wp-content/uploads/sites/9/2019/09/Computationa… The project will involve numerical simulations with Cian O’Donnell (Bristol), mathematical analysis of reduced models with Krasi Tsaneva-Atanasova (Exeter), using electrophysiological and calcium imaging data from genetic animal models of neuropsychiatric disorders collected in the lab of Jeremy Hall (Cardiff). You would apply directly to the MRC GW4 BioMed PhD program (https://www.gw4biomed.ac.uk) which spans Bristol, Cardiff, Exeter and Bath Universities. Application deadline is 25th November and open only to UK or EU citizens or residents (see GW4Biomed site for eligibility details). Please contact Cian O’Donnell (cian.odonnell(a)bristol.ac.uk<mailto:cian.odonnell@bristol.ac.uk>) to discuss before applying. More info on Cian O’Donnell’s group: https://seis.bristol.ac.uk/~co15268 And the lively Bristol Computational Neuroscience Unit: https://bristolcnu.github.io Krasi Tsaneva-Atanasova: https://emps.exeter.ac.uk/mathematics/staff/kt298 Jeremy Hall: https://www.cardiff.ac.uk/people/view/57718-hall-jeremy

1 0

2 Postdocs and 1 Project Manager on H2020 grant
by Michele Giugliano Oct. 11, 2019

Oct. 11, 2019

2 Post-doctoral positions and 1 Project Manager position are available at the newly established Neural Dynamics Laboratory of the International School of Advanced Studies (SISSA) of Trieste, Italy (http://phdneurobiology.sissa.it/eng/faculty/michele-giugliano.aspx <http://phdneurobiology.sissa.it/eng/faculty/michele-giugliano.aspx>). The positions are funded for up to 42 months on a new EC-Horizon 2020 initiative called "Ionic Neuromodulation For Epilepsy Treatment (IN-FET)", combining neurobiology, nanotechnologies, electrochemistry, and electronics together for designing a breakthrough novel technology in brain modulation. The research positions aim to experimentally validate novel routes for cellular and microcircuit stimulation or suppression, in collaboration with a consortium of partners which includes IBM Research Zurich, the University of Geneva, the University of Sheffield, and the Inter-university consortium for Nanoelectronics. We search for experts in in vitro electrophysiology (substrate-integrated microelectrode arrays) and patch-clamp recordings (dissociated cell cultures, acute and organotypic brain tissue slices) with a strong background in quantitative data analysis and a strong interest for interdisciplinary research. The Project Manager position aims at supporting the organization, dissemination, and reporting activities in the context of EC-funded project and partially at supporting scientific software development. We search for candidates with previous experience in management of H2020 project, and fluent with the reporting EC online platform (e.g. Participant Portal) who might also be interested in providing partial support for content management of a web site as well as for scientific software applications development. Please direct informal inquiries, a CV and a brief statement of interest, to Prof. Michele GIUGLIANO (michele.giugliano AT sissa.it) Direct application soon available from the SISSA's website: https://www.sissa.it/recruitment <https://www.sissa.it/recruitment>

1 0

Postdoctoral / Research Specialist position in Neural Circuits and Behavior
by Reiser, Michael Oct. 10, 2019

Oct. 10, 2019

Postdoctoral / Research Specialist position in Neural Circuits and Behavior The Reiser lab at the Janelia Research Campus (https://www.janelia.org/lab/reiser-lab) seeks a creative scientist to join us in figuring out how the fly brain uses visual information to control behavior. We use behavioral, anatomical, imaging, electrophysiological, and computational methods to understand the neural circuits for vision and navigation in Drosophila. This is an exciting time to be working on the fly brain—full brain connectomes and precise genetic access to nearly every cell type in the brain are on the horizon. We pair these tools with high-throughput, high-content exploration of Drosophila behaviors. In this position, you would apply these methods to deeply map behavioral circuits. Many project directions are possible that are related to active research topics in the lab: • visual motion guided behaviors • visual place learning • central modulation of vision Requirements: • A keen interest in figuring out the brain. • Ph.D. in experimental biology, neuroscience, or a quantitative field. • Familiarity with scientific computing environments • Experience in some of these areas: instrumentation, computer vision, and machine learning, neurophysiology, animal behavior, Drosophila molecular/genetic methods, neuroanatomy. Janelia is a unique, exciting research environment near Washington, D.C., with abundant opportunities for collaboration and learning new things. Interested applicants should apply by email; please include your curriculum vitae and research interests and arrange for three letters of reference to be sent to reiserm at janelia.hhmi.org. The Reiser lab is committed to maintaining a diverse and inclusive environment. Members of groups underrepresented in science are especially encouraged to apply. HHMI is an equal opportunity employer.

1 0

PhD position in computational neuroscience with Prof. Laurenz Wiskott in Bochum, Germany
by Laurenz Wiskott Oct. 10, 2019

Oct. 10, 2019

Please forward this job advertisement to candidates who might be interested. Thanks, Laurenz Wiskott. ___________________________________________________________________________ Open position for a PhD student with Prof. Laurenz Wiskott at the Institute for Neural Computation, Bochum, Germany ___________________________________________________________________________ University: The Ruhr-Universität Bochum is one of the leading research universities. The university draws its strengths from both the diversity and the proximity of scientific and engineering disciplines on a single, coherent campus. This highly dynamic setting enables students and researchers to work across traditional boundaries of academic subjects and faculties. Institute: Institute for Neural Computation Ruhr-University Bochum Universitaetsstr. 150 D-44801 Bochum, Germany, EU The Institute for Neural Computation is a central research institute at the Ruhr-University Bochum, see https://www.ini.rub.de/. It focuses on the dynamics and learning of perception and behavior on a functional level but is otherwise very diverse, ranging from neurophysiology and psychophysics over computational neuroscience to machine learning and technical applications. Research group: Prof. Dr. Laurenz Wiskott, see https://www.ini.rub.de/research/groups/theory_of_neural_systems/ Research topics: We are looking for an outstanding candidate who will be working on a system-level model of spatial navigation with the hippocampus as one of its central areas. We use methods from neural networks and machine learning. It is also planned to simulate experiments done with rat and/or mice by our experimental partners. The position is part of a joint team with Prof. Sen Cheng working on developing a system-level model of hippocampal function for memory and navigation. This is being done in close interaction with a team working on similar questions from the machine learning perspective. Teaching: There is a teaching load of 3 hours per week during the semester, in particular for a programming course in python. Time: The appointment will be for three years and can then be extended for one more year if needed. Anticipated starting date is Feb 1st. Requirements: Candidates should have an education (equivalent to a MSc) in computer science, physics, mathematics, electrical engineering or any related field. Required are strong mathematical and programming skills (ideally in python) as well as the ability to communicate and work well in a team. Salary: Salary is 75% of salary scale TV-L E13. Inquiries: Informal inquiries can be addressed to Prof. Laurenz Wiskott <laurenz.wiskott(a)rub.de>. Application: Applications (CV, transcript of records for MSc and BSc, statement of purpose) should be sent as a single pdf file to Prof. Laurenz Wiskott <laurenz.wiskott(a)rub.de>. Ruhr-University Bochum is committed to equal opportunity in employment and gender equality in its working environment. We therefore look forward to applications from qualified women. Applications from appropriately qualified handicapped persons are also encouraged.

1 0

PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia
by Narly Golestani Oct. 10, 2019

Oct. 10, 2019

PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia PhD and Postdoc positions are available at the Brain and Language Lab (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) at the University of Geneva. The PhD position is for 3-4 years, and the postdoc position is for up to 4 years, and salary will be commensurate with experience. Several projects will be done in collaborations with Maastricht University and with the University of Vienna. Applicants should have a strong interest in human brain imaging, and in language function and dysfunction, and should have one of (or a combination of) the following profiles: 1. Candidates with a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and with solid experience in computational modelling (i.e. encoding / decoding) of fMRI data, machine learning, statistics and programming. Projects will include extensions of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) to higher levels of language processing. 2. Candidates with a degree in Cognitive Neuroscience, Biomedical Engineering and/or Psychology, with solid experience in the acquisition and analysis of brain functional (and structural) imaging data. Projects will include real-time fMRI neurofeedback training studies, focusing on different levels/aspects of language learning. Candidates for either position (depending on experience) will also have the opportunity to become involved in the analysis of data from a 7T myelin mapping (R1) study. The positions are available immediately, and applications will be considered until the position is filled. Applicants should send me their CV, a statement of research interests, and the names and contact information for 2-3 references, at Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Prof. Narly Golestani Brain and Language Lab Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

1 0

computational neuroscience PhD positions at Imperial College
by Dan Goodman Oct. 9, 2019

Oct. 9, 2019

Two or more PhD positions in theoretical and computational neuroscience are available in the "Neural Reckoning" group of Dan Goodman at Imperial College London (http://neural-reckoning.org) I am interested in supervising students with a strong mathematical, computational or neuroscience background. Projects could be carried out in several possible areas relating to the work in the group. Some suggestions for topics that would be interesting to me are below, but I'm very happy to consider other possibilities. In addition to working within the group, studying at Imperial College provides excellent opportunities for interacting with other theoretical and experimental researchers, both at Imperial and in the many neuroscience groups in London. At the moment, I'm particularly interested in using techniques from machine learning to generate biologically plausible models that can also perform complex tasks. I'm also generally interested in how to perform computations with spiking neurons, and the computational role of neural mechanisms (such as spiking and heterogeneity). I often work in the auditory system, which is particularly interesting when thinking about temporal processing. Finally, I'm one of the authors of the "Brian" spiking neural network simulator (http://briansimulator.org) and I'm always interested in students who want to work on neuroinformatics projects such as simulation or neural data analysis. For more details, see: http://neural-reckoning.org/openings.html Applicants should initially send me a brief CV and cover letter with a description of research interests or a proposed project, and will eventually have to formally apply through the standard Imperial College mechanism (http://www.imperial.ac.uk/electrical-engineering/study/phd/) I will consider applications as they arrive, so earlier applications are encouraged. EU students from outside the UK are particularly encouraged to apply early because any offer made before Brexit will be respected on the basis of current rules, while the status of offers made after Brexit may be more complicated if a no deal Brexit goes ahead (although this is unlikely as the UK parliament has declared that to be illegal, but you never know). For more information on Brexit: https://www.imperial.ac.uk/about/imperial-and-the-european-union/support-fo… Before applying, please make sure you meet the Imperial College exam grade requirements: * General requirements: https://www.imperial.ac.uk/study/pg/apply/requirements/ * Country-specific minimum grades: https://www.imperial.ac.uk/study/pg/apply/requirements/pgacademic/ Dan Goodman

1 0