- Comp-neuro - lists.cnsorg.org

INCF/OCNS Software WG: Dev sessions on Brian (11th Feb) and NeuroFedora (16th Feb)
by Ankur Sinha 22 Feb '21

22 Feb '21

Hello everyone, Apologies for the cross-posts. The INCF/OCNS Software Working Group (WG)[1] is happy to announce its first set of "Dev sessions" where members of the developer teams of commonly used neuroscience software will introduce their software and then discuss their *development* pipelines. The aim of these sessions is to stimulate discussion of the development practices and tools used by different teams to improve the software we use while also improving our knowledge of these practices and tools. We also hope to encourage more users of these tools to contribute to their development to ensure their longevity. Two sessions are currently scheduled: - Marcel Stimberg will speak about the development of the Brian simulator on Feb 11, 2021 1700 UTC[2]. Zoom link: https://ucl.zoom.us/j/91389216854?pwd=cFVWaXRYVFRUdll2c09Xb3dBS2FWQT09 - Ankur Sinha will speak about the development of the NeuroFedora Linux distribution on Feb 16, 2021 1700 UTC[3]. Zoom link: https://ucl.zoom.us/j/94964460359?pwd=MTJmWEY1NHRxd3l4ZGdtTS9NQ1FaZz09 (To prevent spamming/trolling during these sessions, you will need to login to your Zoom account to join them. These sessions will be recorded and made available for later viewing also.) Sessions on GeNN and Neurolib will also follow shortly. If you develop software for neuroscience, we would love to hear about your development pipeline. Please get in touch with the Software WG either on INCF's Neurostars platform[4] or on our GitHub repository[5]. The WG is a community based group that is open to everyone at all levels of their careers (academic or otherwise). Please introduce yourself to the community on our channels to get involved. [1] https://ocns.github.io/SoftwareWG/pages/about.html [2] https://ocns.github.io/SoftwareWG/2021/02/07/dev-session-marcel-stimberg-br… [3] https://ocns.github.io/SoftwareWG/2021/02/07/dev-session-ankur-sinha-neurof… [4] https://neurostars.org/t/ocns-infrastructure-software-tools-sig-meet-and-gr… [5] https://github.com/OCNS/SoftwareWG/issues On behalf of the WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

1 1

PhD Student position at the interface of neuroscience and machine learning
by Rava A. da Silveira 20 Feb '21

20 Feb '21

The lab of Rava Azeredo da Silveira invites applications for a *PhD Student position* at the *interface of computational neuroscience and machine learning*, at the Institute of Molecular and Clinical Ophthalmology Basel (IOB) in Switzerland, an associated institute of the University of Basel. Research projects will involve modeling and data analysis; some projects will be carried out in the framework of collaborations with experimental labs. Questions will be chosen from a range of topics involving neural representations as relating to behavior, neural coding, dynamics and learning. Candidates with backgrounds in mathematics, statistics, artificial intelligence, physics, computer science, and engineering are welcome. Experience with data analysis and proficiency with numerical methods, in addition to familiarity with mathematical and statistical methods, are desirable. Equally desirable are a spirit of intellectual adventure, eagerness, and drive. The positions will come with highly competitive work conditions and salaries. *Application deadline:* For full consideration, please apply by 15 March 2021. *How to apply:* Please send the following information *in one single PDF, to * *silveira(a)iob.ch* <silveira(a)iob.ch>*:* 1. letter on motivation and interests; 2. curriculum vitæ; 3. transcripts of undergraduate and Master grades. In addition, please arrange for three letters of recommendations to be sent to the same email address. In all email correspondence, please include the mention “APPLICATION-PHD” in the subject header, otherwise the application will *not* be considered. *** *The Silveira** Lab* focuses on a range of topics, which, however, are tied together through a central question: How does the brain represent and manipulate information? Among the more concrete approaches to this question, the lab analyses and models neural activity in circuits that can be identified, recorded from, and perturbed experimentally, such as visual neural circuits in the retina and the cortex. Establishing links between physiological specificity and the structure of neural activity yields an understanding of circuits as building blocks of cerebral information processing. On a more abstract level, the lab investigates the representation of information in populations of neurons, from a statistical and algorithmic—rather than mechanistic—point of view, through theories of coding and data analyses. These studies aim at understanding the statistical nature of high-dimensional neural activity in different conditions, and how this serves to encode and process information from the sensory world. In the context of cognitive studies, the lab investigates mental processes such as inference, learning, and decision-making, through both theoretical developments and behavioral experiments. A particular focus is the study of neural constraints and limitations and, further, their impact on mental processes. Neural limitations impinge on the structure and variability of mental representations, which in turn inform the cognitive algorithms that produce behavior. The lab explores the nature of neural limitations, mental representations, and cognitive algorithms, and their interrelations.

1 0

Postdoc opening at the interface of cognitive science and machine learning
by Rava A. da Silveira 20 Feb '21

20 Feb '21

The lab of Rava Azeredo da Silveira invites applications for a *Postdoctoral Researcher* position at the *interface of theoretical/computational cognitive science and machine learning* at the Institute of Molecular and Clinical Ophthalmology Basel (IOB) in Switzerland, an associated institute of the University of Basel. Research questions will be chosen from a range of topics involving models of decision making, learning, and memory, with a particular focus on the structure of human inference, the nature of internal representations/latent variables, and behavioral variability. While the projects will be primarily theoretical, they will involve data analysis and may be complemented with behavioral experiments or carried out in collaboration with experimental labs. Candidates with backgrounds in mathematics, statistics, artificial intelligence, physics, computer science, engineering, and psychology are welcome. Experience with data analysis and proficiency with numerical methods, in addition to familiarity with neuroscience topics and mathematical and statistical methods, are desirable. Equally desirable are a spirit of intellectual adventure, eagerness, and drive. The positions will come with highly competitive work conditions and salaries. *Application deadline:* For full consideration, please apply by 15 March 2021. *How to apply:* Please send the following information *in one single PDF, to * *silveira(a)iob.ch* <silveira(a)iob.ch>*:* 1. letter of motivation; 2. statement of research interests, limited to two pages; 3. curriculum vitæ including a list of publications; 4. any relevant publications that you wish to showcase. In addition, please arrange for three letters of recommendations to be sent to the same email address. In all email correspondence, please include the mention “APPLICATION-POSTDOC” in the subject header, otherwise the application will *not* be considered. *** *The Silveira** Lab* focuses on a range of topics, which, however, are tied together through a central question: How does the brain represent and manipulate information? Among the more concrete approaches to this question, the lab analyses and models neural activity in circuits that can be identified, recorded from, and perturbed experimentally, such as visual neural circuits in the retina and the cortex. Establishing links between physiological specificity and the structure of neural activity yields an understanding of circuits as building blocks of cerebral information processing. On a more abstract level, the lab investigates the representation of information in populations of neurons, from a statistical and algorithmic—rather than mechanistic—point of view, through theories of coding and data analyses. These studies aim at understanding the statistical nature of high-dimensional neural activity in different conditions, and how this serves to encode and process information from the sensory world. In the context of cognitive studies, the lab investigates mental processes such as inference, learning, and decision-making, through both theoretical developments and behavioral experiments. A particular focus is the study of neural constraints and limitations and, further, their impact on mental processes. Neural limitations impinge on the structure and variability of mental representations, which in turn inform the cognitive algorithms that produce behavior. The lab explores the nature of neural limitations, mental representations, and cognitive algorithms, and their interrelations.

1 0

Valentin Braitenberg Award for Computational Neuroscience - call for nominations!
by Alexandra Stein 18 Feb '21

18 Feb '21

Dear Colleagues, The Bernstein Network Computational Neuroscience invites nominations for the Valentin Braitenberg Award for Computational Neuroscience. The Bernstein Network presents the award biennially to a scientist in recognition of outstanding research that contributes to the understanding of the functioning of the brain. The major criterion for the award is the impact or potential impact of the recipient's research on the field of brain science. In the spirit of Valentin Braitenberg's own research, special emphasis is given to theoretical studies elucidating the functional implications of brain structures and their neuronal network dynamics. The awardee receives €5.000 prize money, donated by the Autonome Provinz Bozen Südtirol, as well as a Golden Neuron pin. The award will be presented in a special award ceremony at the online Bernstein Conference 2021, followed by a keynote lecture of the Braitenberg Awardee. Nominations may be submitted by scientists working in the field of computational neuroscience and should include the following documents: - One-page laudation, in which the scientific work of the candidate is honored with regard to the award criteria - CV and list of publications Deadline for nominations is April 30, 2021 by email to a.stein(a)fz-juelich.de<mailto:a.stein@fz-juelich.de> Please note that self-nominations are not permitted. The call for nominations can be found under the following URL: https://www.bernstein-network.de/en/the-network/awards/Call_Braitenberg_2020<http://www.nncn.de/en/bernstein-conference/2018/braitenberg_award> For inquiries please contact a.stein(a)fz-juelich.de<mailto:a.stein@fz-juelich.de>. Best regards, Alexandra Stein -- Dr. Alexandra Stein Head of Bernstein Coordination Site Bernstein Network Computational Neuroscience | Bernstein Coordination Site (BCOS) Branch Office of the Forschungszentrum Jülich at the University of Freiburg Hansastr. 9A | 79104 Freiburg, Germany phone: (+49) 0761 203 9583 mobile: (+49) 0151 67114645 mail: a.stein(a)fz-juelich.de<mailto:a.stein@fz-juelich.de> web: www.bernstein-network.de<http://www.bernstein-network.de> Twitter: BernsteinNeuro YouTube: Bernstein TV LinkedIn: Bernstein Network Computational Neuroscience, Germany ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Faculty Position in Comp-Neuro / ML at Champalimaud - Deadline February 28, 2021
by Christian Machens 18 Feb '21

18 Feb '21

Faculty Position in Computational Neuroscience / Machine Learning at Champalimaud Research - Deadline February 28, 2021 The Champalimaud Foundation (CF) invites applications for Group Leaders to join a dynamic and highly collaborative international research institute in Lisbon, Portugal. Champalimaud Research (CR) is seeking to expand its Neuroscience Programme (CNP) with one Junior Group Leader (Assistant Professor equivalent). About you We welcome applicants with expertise in modern Machine Learning and Artificial Intelligence. Suitable research areas for the recruited applicant include statistical methods for complex, high-dimensional datasets, artificial neural networks, computer vision, reinforcement learning, and control theory. We will consider candidates that work on foundational issues in these fields, as well as candidates who take more applied approaches. The ideal candidate should present a research program with both fundamental research and applied elements, and have a strong desire to collaborate with existing teams within CR and CF, including the Champalimaud Clinical Centre. Special attention will be given to applications of individuals from underrepresented groups. About the position To promote risk-taking research, generous support for salary, start-up and annual running costs will be provided. Researchers will be based at the Champalimaud Centre for the Unknown (CCU), a highly interactive and innovative scientific environment where the Neuroscience Programme is composed of groups applying a range of theoretical and experimental approaches to understand the algorithmic, physiological and circuit mechanisms of behaviour. Researchers routinely collect rich datasets ripe for development and application of new analysis tools or comparison with theory. These datasets include high dimensional neurophysiological and imaging data, to -omics, and various measures of behaviour. About us The Champalimaud Centre for the Unknown is situated on the waterfront in Lisbon. English is the official language of the Centre. Lisbon has a sunny Atlantic-Mediterranean climate, vibrant culture, international schools, convenient housing options and is considered one of the world’s safest cities. About the application Applications should include a (1) detailed scientific curriculum vitae, which may include any mentoring, outreach, or policy experiences, (2) a brief summary of past accomplishments (max. two pages), (3) a description of future research plans (max. four pages), (4) three key publications (pdf-files preferred, preprints welcome) along with (5) brief (~200 word each) descriptions of their significance, and (6) contact details for three individuals who can provide recommendation letters upon request. Applications or informal inquiries should be addressed to careers(a)research.fchampalimaud.org <mailto:careers@research.fchampalimaud.org> with the subject “Neuro GL Call 2020 – YOUR LAST NAME”. The deadline for the applications is February 28, 2021 and review of applications will begin in March, 2021. Non-discrimination and equal access policy The Champalimaud Foundation actively promotes non-discrimination and equal access, so that no candidate may be privileged, favored, prejudiced or deprived of any right or excluded from any duty on the basis of age, sex, gender identity, sexual orientation, race/ethnicity, disability, chronic illness, language, nationality, territory of origin, family status (marital, pregnancy and maternity, having or not having dependents), socioeconomic situation, education, religion, political or ideological beliefs, trade union membership, or on any other grounds which are not deemed relevant for the performance of the duties associated with the advertised position.

1 0

INCF/OCNS Software WG: Dev session on Neurolib (23rd Feb)
by Ankur Sinha 18 Feb '21

18 Feb '21

Hello everyone, Apologies for the cross-posts. The INCF/OCNS Software Working Group (WG)[1] is happy to announce the next "Dev session" on Neurolib[2] where Caglar Cakan will introduce the software and then discuss its *development* pipeline. The session will be held on Feb 23, 2021 at 1700 UTC[3]. Zoom link: https://tu-berlin.zoom.us/j/68960683644?pwd=a2JTTS8xZXhwY0ZtQ0J0aktRVW52Zz09 The aim of these sessions is to stimulate discussion of the development practices and tools used by different teams to improve the software we use while also improving our knowledge of these practices and tools. We also hope to encourage more users of these tools to contribute to their development to ensure their longevity. The abstract of the talk is below: neurolib is a computational framework for whole-brain modelling written in Python. It provides a set of neural mass models that represent the average activity of a brain region on a mesoscopic scale. In a whole-brain network model, brain regions are connected with each other based on structural connectivity data, i.e. the connectome of the brain. neurolib can load structural and functional data sets, set up a whole-brain model, manage its parameters, simulate it, and organize its outputs for later analysis. The activity of each brain region can be converted into a simulated BOLD signal in order to calibrate the model to empirical data from functional magnetic resonance imaging (fMRI). Extensive model analysis is possible using a parameter exploration module, which allows to characterize the model’s behaviour given a set of changing parameters. An optimization module allows for fitting a model to multimodal empirical data using an evolutionary algorithm. Besides its included functionality, neurolib is designed to be extendable such that custom neural mass models can be implemented easily. neurolib offers a versatile platform for computational neuroscientists for prototyping models, managing large numerical experiments, studying the structure-function relationship of brain networks, and for in-silico optimization of whole-brain models. ----- If you develop software for neuroscience, we would love to hear about your development pipeline. Please get in touch with the Software WG either on INCF's Neurostars platform[4] or on our GitHub repository[5]. The WG is a community based group that is open to everyone at all levels of their careers (academic or otherwise). Please introduce yourself to the community on our channels to get involved. [1] https://ocns.github.io/SoftwareWG/pages/about.html [2] https://neurolib-dev.github.io/ [3] https://ocns.github.io/SoftwareWG/2021/02/12/dev-session-caglar-cakan-neuro… [4] https://neurostars.org/t/ocns-infrastructure-software-tools-sig-meet-and-gr… [5] https://github.com/OCNS/SoftwareWG/issues On behalf of the WG, -- Thanks, Regards, Ankur Sinha (He / Him / His) Research Fellow at the Silver Lab | http://silverlab.org/ Department of Neuroscience, Physiology, & Pharmacology University College London, London, UK Time zone: Europe/London

1 0

two faculty positions at Imperial College in 'intelligent systems' (deadline March 1st)
by Goodman, Daniel F M 18 Feb '21

18 Feb '21

We are hiring two new faculty positions in the Electrical Engineering department at Imperial College, deadline March 1st. The advert below talks about machine learning and computer vision, but actually we're open to anything that will complement the existing interests of our group (robotics, machine learning, computational neuroscience). In particular, we're looking for people who can develop new collaborations with our group, so interdisciplinary researchers touching on any of these topics please do apply! I'd also like to add that we'd particularly encourage applications from women and other groups that are underrepresented in our department. https://www.imperial.ac.uk/jobs/description/ENG01538/lecturersenior-lecturer Please do feel free to get in touch for more info. Dan

1 0

15 PhD positions translational vision science, OptiVis
by Peter König 17 Feb '21

17 Feb '21

15 PhD positions in Translational Vision Science It is essential to know what visually impaired individuals can do with their residual vision in daily life activities, otherwise known as their "functional vision". Conventional ophthalmic tests (e.g. visual field tests) are able to detect the extent of a visual defect, but they yield little information about functional vision. This lack of appropriate tests impedes the optimal practice of diagnostics (in ophthalmic and neurological care, in particular of children and elderly), rehabilitation and classification (essential in sports competitions). Our European MARIE SKŁODOWSKA-CURIE Innovative Training Network (ITN) OptiVisT aims to resolve this by (1) gaining new Insights: i.e. a fundamental understanding of the visual demands of activities of daily living and sports; (2) developing Solutions: i.e. creating new objective, inclusive and engaging tools for testing, training and augmenting functional vision; and (3) the Application of 1 and 2: evaluating the effectiveness of our new tools in diagnostics, rehabilitation and classification in practice. Are you, like us, fascinated by vision, the brain and technology and consider it important to help visually impaired people? Do you have an inquisitive mind, and are you looking for a PhD position embedded in an international innovative training network in which you can develop your research, technical or clinical skills? Then consider applying with OptiVisT and join one of our 15 PhD projects (overview below). We offer PhD positions in academia, medical, technology and rehabilitation institutes, and high-tech companies. Curious to see and hear more about what it means to be part of such Innovative Training Network? Check out these two short movies about our previous ITNs NextGenVis and EGRET+. If you are interested in one of our PhD positions, visit our website (www.optivist.eu) for more information on our application procedures. The deadline for applying for this project is February 28th, 2021. General questions can be directed to info(a)optivist.eu. Project specific questions can be directed to the project contacts as mentioned on the website. Best, Peter König (on behalf of the Optivis Consortium)

1 0

Research Topic in Frontiers in Neuroprosthetics
by Marianna Semprini 16 Feb '21

16 Feb '21

Dear colleagues, We are excited to announce a Research Topic in Frontiers in Neuroscience - section Neuroprosthetics titled "Improving Neuroprosthetics through Novel Techniques for processing Electrophysiological Human Brain Signals". This research topic focuses on innovative approaches for translating current research results into useful clinical applications providing novel therapeutic possibilities in the neurorehabilitation and neuroprosthetic field. The development of these novel solutions could help people with disabilities to overcome their daily obstacles and achieve a better quality of life. We are thus widely open to contributions that target: * novel experimental designs, clinical protocols, and applications involving brain signals in the context of neurorehabilitation; * techniques for off-line signal processing, e.g. investigation of brain activity (EEG, EcoG, stereo-EEG, MEG), characterization of brain oscillations, decoding of information in the brain (e.g. sensory and/or motor); * techniques for on-line signal processing, e.g. novel hardware design for treating human brain signals; * assessment of plastic changes following a neurorehabilitation treatment or upon usage of a prosthetic device, e.g. novel biomarkers based on electrophysiological recordings, computational models for understanding reconfiguration mechanisms; * standardized methods to store and process data, in agreement with the FAIR principles. We accept submissions of manuscripts as Original Research, Systematic Review, Review (and mini-Review), Perspective, Clinical Trial, Case Report, Brief Research Report. Deadline for manuscript submission is June 5th, 2021. More information can be found here<https://www.frontiersin.org/research-topics/18352/improving-neuroprosthetic…>. We look forward to your contributions. The Research Topic co-editors, Marianna Semprini Gabriele Arnulfo Ioannis Delis Felix Siebenhühner Gianluca Susi Marianna Semprini, PhD Rehab Technologies IIT-INAIL Lab Phone : 010 71781 212 ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 Genova Site: www.iit.it

1 0

10 PhD/Postdoc positions on metrology for AI in medicine at PTB Germany
by Haufe, Stefan 16 Feb '21

16 Feb '21

Dear colleagues, I would be grateful if you could circulate the following announcement. Ten PhD or Postdoc positions are available at the German national metrology institute (PTB) in Berlin and Braunschweig: Topics are centered around metrological aspects (robustness, uncertainty, interpretability) of artificial intelligence in medicine. This includes projects on M/EEG and fMRI inverse problems as well as explainable AI in neuroscience. Please go to is.gd/WYHec1 for details and instructions on the application process. Further information is available under the following links: * on the general research program these positions are embedded in: is.gd/24hYaD * on PTB's AI strategy for medicine: is.gd/Y0cYWv * press release: is.gd/ukCIh9 Candidates specifically interested in one of the first three projects 1. Towards standardized quality control for artificial intelligence systems in critical care (is.gd/HpWzAh) 2. Machine learning and uncertainty quantification for bioelectromagnetic inverse solutions and signal separation methods (is.gd/cdWi1E) 3. Advancing the theory and practice of machine learning model explanations in biomedicine (is.gd/3iPwnu) are encouraged to get in touch with me through haufe_ptb_applications at mailbox dot org . Best wishes, Stefan Haufe

1 0