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INCF/OCNS Software WG: Dev sessions on Brian (11th Feb) and NeuroFedora (16th Feb)

by Ankur Sinha

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

Feb. 8, 2021

Postdoctoral positions at NIPS in Japan: Computational modeling of synaptic biochemical signaling

by Hidetoshi URAKUBO

Dear researchers: We invite applications for a postdoctoral researcher in the area of mathematical/computational modeling of biochemical signaling in neuronal synapses. Based on a grant (#), A new collaborative project with Kyoto U and Nagoya U has been launched for the modeling of liquid-liquid phase separation (LLPS) of synaptic molecules. The successful candidate will develop computational/theoretical models that describe the LLPS and simulate the spatiotemporal dynamics of synaptic biochemical signaling, to elucidate how our learning and memory are organized. We expect who will conduct Monte Carlo simulation under the scheme of the Flory-Huggins (FH) theory, as well as the reaction-diffusion simulation of biochemical molecules. (#) Spatiotemporal dynamics of intracellular components, CREST, Japan Science and Technology Agency (JST), Japan. https://www.jst.go.jp/kisoken/crest//en/research_area/ongoing/area2020-1.ht… We are also conducting a long-standing project on electron microscopic (EM) connectomics. We will welcome the applicants who can contribute to this project from the informatics aspect. National Institute for physiological science (NIPS) is a high-quality national institute for neuroscience in Japan, like Riken CBS. NIPS is located in Aichi prefecture, the middle part of Japan. https://www.nips.ac.jp/eng/ https://en.wikipedia.org/wiki/Aichi_Prefecture http://www2.aia.pref.aichi.jp/tope/foreigner.html Please feel free to ask questions about this research position to Hidetoshi Urakubo (urakubo(a)nips.ac.jp) 1. Job title Full-time Postdoctral Researcher 2. Begin date April 1st 2021 (negotiable) 3. Appointment period Annually renewed based on evaluation. Up to Sep/2025. 4. Workplace NIPS, Okazaki, Japan http://www.nips.ac.jp/circuit/ 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan 5. Qualifications Applicants must: - have Ph.D. (or be near the completion of the degree). - have strong motivations and ambitions to participate in the research above. 6. Compensation Salary will be commensurate with qualifications and experience. Social insurance will be applied. Days off include public holidays, New Year's holidays (Dec. 29 - Jan 3), summer vacation, and sick leave. These and other provisions are in accordance with NIPS regulations. Please inquire it with your CV if the salary information is needed at the early stage of selection. 7. Required documents Please send the following five materials to the email address below: 7-1. Complete CV 7-2. List of publications 7-3. Reprints of 1 to 3 major publications 7-4. Document (one or two pages in A4 or letter size) describing: - Summary of your previous research - Interests and proposal for research - Technical skills (programming skills, etc) 7-5. Two letters of recommendation (including one from the current supervisor, if available) 8. Deadline February 28 (Sun), 2021 (will be extended) 9. Selection Selection will be made based on application screening and interviews. 10. Application and Contact Hidetoshi Urakubo, Ph.D. Email: urakubo(a)nips.ac.jp Project Assistant Professor, Division of Cerebral Circuitry, Department of Fundamental Neuroscience, National Institute for Physiological Sciences (NIPS), 5-1 Myodaiji-Higashiyama, Okazaki, Aichi, 444-8787, Japan Phone: +81-564-59-5280 https://researchmap.jp/urakubo?lang=en http://www.nips.ac.jp/circuit/

Feb. 8, 2021

Special issue: Information Processing in Neuronal Circuits-Journal Biology

by alireza valizadeh

CFP: Special issue on “*Information Processing in Neuronal Circuits and Systems*” Dear colleagues, Together with Claudio Mirasso we are organizing a special issue in the journal “Biology” on the topic “*Information Processing in Neuronal Circuits and Systems*”. We would like to invite you to contribute your research to this special issue. For more information please visit the website https://www.mdpi.com/journal/biology/special_issues/neuronalcircuits Submission deadline: *7 May, 2021*. *Special Issue Information* The question of how the brain integrates the multiplicity of local processes dispersed throughout its entire anatomy is a fundamental question in neuroscience. Such integration is mediated by information exchange between brain areas, and other parts of the nervous system, through routes that can change rapidly to provide a flexible effective connectivity despite the rigidity of the anatomical connections. The flexibility of the information routing and effective connectivity are consequences of the multi-stability of the collective dynamics of the neuronal networks. In other words, a single structural connection can support plenty of degenerate dynamic states for each of which a special pattern of information transfer between the nodes can take place. Collective neuronal oscillations are hypothesized to provide such a basis for the dynamic communication between brain regions. In this Special Issue, the notion of information transfer and routing in neuronal circuits and systems will be addressed with a focus on shedding light on the mechanisms that regulate information transmission in the brain and in the nervous system in general. Please contact us in case you need more information about this special issue. Best, Alireza Valizadeh Topic editors: Claudio R. Mirasso, Universitat Illes Balears, Instituto de Física Interdisciplinar y Sistemas Complejos, Spain (claudio(a)ifisc.uib-csic.es) Alireza Valizadeh, Institute for advanced Studies in Basic Sciences, Iran ( valizade(a)iasbs.ac.ir) -- ------------------------------------------------------------------------ Alireza Valizadeh Associate professor Neurophysics lab, Institute for Advanced Studies in Basic Sciences (IASBS) School of cognitive sciences, Institute for research in fundamental sciences (IPM) Zanjan, Iran Tel:(+98) 24 3315 2120 Fax:(+98) 24 3315 2104 valizade(a)iasbs.ac.ir Web: http://www.iasbs.ac.ir/~valizade/index.html ------------------------------------------------------------------------

Feb. 8, 2021

PhD studentship on “Computational modelling of spiking neural network self-organization” at the University of Surrey (UK)

by roman bauer

*Computational modelling of spiking neural network self-organization* A PhD studentship is available in the lab of Dr Roman Bauer at the Department of Computer Science at the University of Surrey (Guildford, UK). The successful candidate will use computer simulations to study how spiking neural networks can give rise to function, such as classification/prediction of spatio-temporal (visual or auditory) signals. This will contribute to novel technologies for neurally inspired computing, and help shine light shine on how neuronal circuits in the brain operate. This particular PhD studentship will be conducted in co-operation with the BioDynaMo collaboration, where open-source code for the neuroinformatics/computational neuroscience research community is developed. Successful applicants will become part of a vibrant PhD community and will benefit from the strong research environment and high international visibility of the Department. Its researchers publish regularly in top conferences and journals and are renowned experts in their fields, developing innovative, practical solutions to real world problems. The Department has strong links with industry and active collaborations with academic institutions worldwide. *Background:* The ideal candidate will have experience in computer science / physics / mathematics or similar. Proficiency in an object-oriented programming language is required. Previous experience in the modelling and simulation of spiking neural networks would be desired. *Funding:* Each PhD studentship comes with a stipend of £16,000 per annum plus tuition fees covered for the duration of 3 years for UK/EU candidates. International candidates are welcome to apply but will need to cover the difference between the UK/EU and overseas fees. More details including instructions for the application can be found at: https://www.surrey.ac.uk/fees-and-funding/studentships/phd-studentships-com…. Interested candidates are encouraged to contact the lead supervisor Dr Roman Bauer (r.bauer(a)surrey.ac.uk) Application deadline is 21st of February, 2021.

Feb. 7, 2021

Focus on Criticality and Complexity in Brain Dynamics

by Claudius Gros

Dear colleagues A short reminder: Together with Dante Chialvo, we are editing a Focus on Criticality and Complexity in Brain Dynamics Journal of Physics: Complexity Deadline 30 April 2021 https://iopscience.iop.org/journal/2632-072X/page/Focus_on_Criticality_and_… exity_in_Brain_Dynamics Among others, we are especially interested in compact perspectives, e.g. on -- experimental and theoretical methodology -- 'critical' assessments of underlying concepts -- controversial viewpoints We hope that the focus on brain criticality and complexity will be a place to assess where the field stands and where the fields needs to go. Please do not hesitate to contact us for any further information. We are looking forward to your contribution! Claudius Gros ### ### Prof. Dr. Claudius Gros ### http://itp.uni-frankfurt.de/~gros ### ### Complex and Adaptive Dynamical Systems, A Primer ### A graduate-level textbook, Springer (2008/10/13/15) ### ### Life for barren exoplanets: The Genesis project ### https://link.springer.com/article/10.1007/s10509-016-2911-0 ###

Feb. 5, 2021

Open Position: Post-Doctoral Fellowship in Reproducible Neuroimaging Analysis

by Sean Hill

The Krembil Centre for Neuroinformatics has an open position for a postdoc with experience in neuroimaging and software engineering: "Post-Doctoral Fellowship in Reproducible Neuroimaging Analysis” The Krembil Centre for Neuroinformatics (PI Dr. Sean Hill, http://krembilneuroinformatics.ca/)Toronto, is looking to hire a Post-Doctoral Fellow with a strong background in Neuroimaging and Software Engineering. The successful candidate shall spearhead the group's efforts in developing a comprehensive open science platform that captures a range of experimental data, produces a semantic representation that links related scientific content, and provides users with data discovery tools. Working jointly between the Krembil Centre and Radiologics, the successful candidate will be involved cutting-edge development an electronic laboratory notebook platform that enables reproducible human neuroscience workflows. This work will support a global collaborative effort for Accelerating research on Consciousness: An adversarial collaboration to test contradictory predictions of Global Neuronal Workspace and Integrated Information Theory. Led by Dr. Lucia Melloni research on consciousness by providing decisive, field-transformative evidence in favor of one this project will accelerate theory and against the other. It will also establish a groundbreaking model for scientific practices in cognitive neuroscience at large, by demonstrating the impact of team-based adversary research and open data. This will address major riddles in the field, much like established practices in other fields such as physics and genomics have done. Thus, this project may dramatically change the landscape of research—that is, the social practices and norms—in the field of cognitive neuroscience. https://www.templetonworldcharity.org/projects -database/accelerating-research-consciousness- adversarial -collaboration-test-contradictory The platform will enable researchers to define their experiment protocols, capture and manage experiment metadata associated with these protocols, and publish the resulting data sets to a semantically enabled search engine. The platform will provide the basis for creating interactive publications from which each analysis result and figure is linked through structured provenance record to its original source data and analysis pipelines. • To develop an open source electronic laboratory notebook to support reproducible analysis of data that encompasses the most commonly used techniques in human neuroscience: fMRI, MEG, EEG and ECoG. • To develop standards for data annotation and exchange of data and metadata. • To publish those metadata via a semantically-enabled search engine. • The platform will build on several key components. The e -notebook will advance the pilot software currently in development and will include a user-friendly app-based interface to define the structure and content of experiments including the most common cognitive neuroscience experimental methods (fMRI, EEG, MEG, and ECOG). • The system will integrate XNAT, developed in Dr. Marcus’ laboratory at Washington University andatRadiologics(Marcusetal,2007) and BlueBrainNexus(bluebrainnexus.io)platform developed by a team led by Dr. Hill (Kaufmann et al., 2018). XNAT and Nexus are widely-used, open source applications that have been instrumental in advancing reproducible science. The successful candidate will have a PhD in neuroscience, engineering, physics, psychology, or related area, a track record for independent research, and a strong publication record. Strong programming skills and familiarity with neuroimaging data (s/d/fMRI and/or M/EEG) are required; experience with software development, semantic databases and data models are advantageous. For inquiries, please email David Rotenberg (David.Rotenberg(a)camh.ca) with the title “Post-Doctoral Fellowship Reproducible Neuroimaging Platform” in the subject line." https://www.camh.ca/en/science-and-research/institutes-and-centres/krembil-… — Sean Hill, Ph.D. Scientific Director, Krembil Centre for Neuroinformatics Senior Scientist, Campbell Family Research Institute Centre for Addiction and Mental Health Professor, University of Toronto Faculty Affiliate, Vector Institute for Artificial Intelligence Infrastructure Co-lead, University of Toronto Temerty Centre for Artificial Intelligence Research and Education in Medicine (T-CAIREM) Titular Professor, École polytechnique fédérale de Lausanne, Switzerland KrembilNeuroinformatics.ca CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

Feb. 5, 2021

Open postdoc position in plasticity in action execution (Washington DC)

by Ella Striem-Amit

*Postdoctoral researcher position in plasticity in action execution* The SAMP Lab (Sensory and motor plasticity, Ella Striem-Amit’s lab) at Georgetown University (Washington DC, USA) is looking for a passionate and dedicated Postdoctoral researcher to work on a project on plasticity and abstractness in action execution. The SAMP lab explores the balance between innate brain organization and experience-dependent plasticity by studying models of sensory and motor deprivation using behavioral and fMRI state of the art analytical techniques. Specifically, in this project we will explore neural action representations which are independent from the body part used to execute them, studying people born without hands. For detail of the lab see *samp-lab.facultysite.georgetown.edu <http://samp-lab.facultysite.georgetown.edu/>*, and a relevant recent publication: *www.pnas.org/content/117/45/28433 <http://www.pnas.org/content/117/45/28433>*. Excellent understanding of and experience with fMRI and data analysis are required. Strong programming skills (Matlab/R/python, etc.) are also a requirement. Experience with behavioral methods used in motor control and mapping is desirable but not a requirement. The position is not limited to US citizens. The start date is flexible, but preferably May-July 2021.This position is available for two years, and can be extended further based on performance. To apply, please send your CV, a brief statement of research interests and a copy of your recent, representative publication by email to Dr. Ella Striem-Amit (*Ella.StriemAmit(a)georgetown.edu <Ella.StriemAmit(a)georgetown.edu>*) with the subject line: “post-doc application”. Georgetown University is an Equal Opportunity/Affirmative Action Employer fully dedicated to achieving a diverse faculty and staff. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, color, religion, national origin, age, sex, disability status, protected veteran status, or any other characteristic protected by law. -- *Ella Striem-Amit (she/her)* Sensory and Motor Plasticity (SAMP) Lab Edwin H. Richard and Elisabeth Richard Assistant Professor Department of Neuroscience Georgetown University Medical Center 3970 Reservoir Rd., NW Washington, DC 20007 http://samp-lab.facultysite.georgetown.edu/

Feb. 5, 2021

[2nd BCI-UC] Program online

by Moritz Grosse-Wentrup

Dear colleagues: The program of the 2nd BCI-UC on February 10th & 11th 2021 from 03:00 pm to 08:00 pm (CET) is now online: https://bciunconference.univie.ac.at/2nd-bci-uc/ All presentations are streamed live and free-of-charge via https://www.crowdcast.io/e/2nd-brain-computer-interface-unconference/ The 2nd BCI-UC features keynotes by *Camille Jeunet* on "User-centered approach to improve BCI efficiency and usability: Stakes, Progress and Obstacles" and by *Marco Congedo* on "Recent Advances on Riemannian Transfer Learning". In addition, we have twelve contributed presentations on a broad range of topics and a symposium on commercial perspectives for BCI technologies. The BCI-UC committee: Moritz Grosse-Wentrup Anja Meunier Philipp Raggam Jiachen Xu

Feb. 5, 2021

Postdoctoral Position in Computational Neuroscience at the Institute for Neural Computation

by Vinita Samarasinghe

*Pending funding approval*, Prof. Sen Cheng, Institute for Neural Computation at the Ruhr University Bochum, invites applications for a full time (currently 39.83 hours/week) *Postdoctoral position (TV-L E13) in Computational Neuroscience <https://www.ini.rub.de/the_institute/jobs/postdoctoral_position_in_computat…>. * The position starts 01.07.2021 and is funded for three years. *Job description* The position is part of the Collaborative Research Center “Extinction Learning” (SFB 1280) and expected to study the principles underlying spatial learning and its extinction with reinforcement learning models. A particular focus is the role of episodic-like memory in learning and extinction processes. The research group is highly dynamic and uses diverse computationalmodeling approachesincludingbiological neural networks, cognitive modeling, and machine learning to investigatelearning and memory in humans and animals. For further information see www.rub.de/cns <http://www.rub.de/cns>. *Your Profile: * Candidates must have * a doctorate degreein neuroscience, physics, mathematics, electrical/biomedical engineering or a closely related field, * relevant experience in mathematical modeling, * excellent programming skills (e.g., Python, C/C++, Matlab), * excellent communication skills in English * the ability to work well in a team. Research experience in neuroscience would be a further asset. The Ruhr University Bochum is home to a vibrant research community in neuroscienceand cognitive science. The Institute for Neural Computation is an independent research unit and combines different areas of expertise ranging from experimental and theoretical neuroscienceto machine learning androbotics. Please send your application, including CV, transcripts and research statement electronically, as a single PDF file, to samarasinghe(a)ini.rub.de <mailto:samarasinghe@ini.rub.de>. In addition, at least two academic references mustbe sent independently to the above email address. The deadline for applications is April11^th , 2021. Travel costs for interviews will not be reimbursed. The Ruhr University Bochum is committed to equal opportunity. We strongly encourage applications from qualified women and persons with disabilities. We are committed to providing a supportive work environment for female researchers, in particular those with young children. Our university provides mentoring and coaching opportunities specifically aimed at women in research. We have a strong research network with female role models and will provide opportunities to networkwith them. Wherever possible, events will be scheduled during regular childcare hours. Special childcare will be arranged if events have to be scheduled outside of regular hours, in case of sickness and during school or daycare closures. Where childcare is not an option parents will be offered a home office solution. -- Vinita Samarasinghe M.Sc., M.A. Science Manager Arbeitsgruppe Computational Neuroscience Institut für Neuroinformatik Ruhr-Universität Bochum, NB 3/26 Postfachnummer 110 Universitätstr. 150 D-44801 Bochum Tel: +49 (0)234 32 27996 Email: samarasinghe(a)ini.rub.de

Feb. 5, 2021

FENS job advertisement for Executive Director position

by Helena Ledmyr

The Federation of European Neuroscience Societies, FENS, seeks an outstanding association executive or executive‐scientist to serve as its next Executive Director. The new Executive Director should have experience in leading a scientific organisation, knowledge of current trends and issues facing life sciences and particularly neuroscience, and understand the legislative process and public policy, as well as the financial tenets of a non‐profit organisation. This is a full-time position based in Brussels, Belgium. Reviewing of applications will begin on 15 February 2021 and applications will be accepted until the position has been filled. https://www.fens.org/News-Activities/News/2021/02/FENS-ED-position/ All the best Helena ----------------------------- Helena Ledmyr, PhD *Director* *Development and Communications* International Neuroinformatics Coordinating Facility Secretariat Karolinska Institutet. Nobels väg 15A, SE-171 77 Stockholm. Sweden Email: helena.ledmyr(a)incf.org Phone: +46 8 524 870 35 incf.org neuroinformatics.incf.org

Feb. 4, 2021