December 2021 - Comp-neuro - lists.cnsorg.org

INCF endorses a new FAIR software best practice!

by INCF

*INCF endorses the Five Recommendations for FAIR Software as a Best Practice* The Five Recommendations for FAIR Software <https://fair-software.eu/> aim to encourage the greater adoption of FAIR principles by providing a set of starting recommendations that researchers can use to improve the quality, reach, and reproducibility of their software. The recommendations were created by The Netherlands eScience Center <https://www.esciencecenter.nl/> and DANS <https://dans.knaw.nl/en/>, the Dutch national centre of expertise and repository for research data. The Five Recommendations for FAIR Software were endorsed on November 30, 2021, after a public comment period and review by the INCF SBP committee. Find their use cases here <http://bit.ly/SBP5recommendations>. Learn more about the recommendations here <https://bit.ly/5recommendationsblog>. /The INCF Secretariat

Dec. 2, 2021

Video recording from Online Workshop "Towards multipurpose neural network models II: Model testing and model fitting"

by Zélie Tournoud

Dear colleagues, We are happy to inform you that the video recordings from the *Workshop on "Towards multipurpose neural network models II: Model testing and model fitting" *are now available to watch online: See the playlist here. <https://www.youtube.com/playlist?list=PLGAiaveljnk9yz_vMjlZckOMnObk1WtlJ> ** **It took placefrom 30 September to 01 October 2021 and has been organized by Anton Arkhipov (Allen Institute, Seattle), Gaute Einevoll (NMBU/University of Oslo), with the support of the European Institute for Theoretical Neuroscience. We hope the content for these videos will be of interest for you. Kind regards, *Zélie Tournoud*/ Communication manager at EITN/ *European Institute for Theoretical Neuroscience (EITN)* UMR 9197 – *NeuroPSI*(Institut des Neurosciences Paris-Saclay) CNRS – Université Paris-Saclay 151 route de la Rotonde Bâtiment 151 91400 Saclay https://www.eitn.org */Mailing address:/*/// UMR 9197 NeuroPSI BP 45 – 91940 Les Ulis Courtaboeuf/ **

Dec. 2, 2021

Doctoral position on foraging dynamics in natural environment.

by Ahmed El Hady

We are offering a PhD position at the International Max planck Research School for Quantitative Behavior, Ecology and Evolution from lab to field (IMPRS-QBEE) situated in the beautiful German town of Konstanz. It is a newly established highly interdisciplinary school that brings a full breadth of expertise from ecology to physics to computer science to neurobiology in order to understand animal behavior across the whole animal kingdom . For more information about the school, please check this website: https://www.ab.mpg.de/3228/imprs . The deadline for application is mid-january 2022: https://www.ab.mpg.de/406326/applications-2022 The PhD project I am offering is a joint project between my group and the group of Einat Couzin , both situated at the Center for advanced study of collective behavior and the Max Planck institute of Animal Behavior in Konstanz. Below are the details of the project ( https://www.ab.mpg.de/426580/Couzin-Fuch_El-Hady ): Foraging is a universal, evolutionary conserved, behavior as animals in nature forage in groups across large spaces looking for resources to satisfy their energetic needs. To date, laboratory experiments have been constrained to animals foraging in small spaces and in small groups. There is an increasing evidence that both neural and behavioral dynamics, however, are principally different in natural spatial scales. The project aims to investigate basic principles underlying foraging decisions in large-scale dynamic environments, that mimic natural habitats. We will focus on two very different model organisms, each exhibits different adaptations to foraging under conditions of considerable uncertainty: swarm-forming locusts and rats. The experiments will be performed at the imaging hangar in the visual computing of collective building at Konstanz University. The imaging hangar is the largest indoor animal imaging facility in the world, offering the opportunity to perform foraging experiments at an unprecedented scale. Using patch foraging as a quintessential behavioral paradigm, and a combination of high throughput continuous video tracking and quantitative modeling approaches, we aim to elucidate how foraging strategies are updated in a changing social and physical world. You will join our interdisciplinary team at the Max Planck Institute for Animal Behaviour (https://www.ab.mpg.de/) and the Excellence Cluster for the Advanced Study of Collective Behaviour (www.exc.uni-konstanz.de/collective-behaviour) The Max Planck Society and Konstanz University are equal opportunity employers that are committed to provide employment opportunities to all qualified applicants without regard to race, color, religion, age, nation, sexual orientation, gender identity, or disability. They seek to increase the number of women in those areas where they are underrepresented and therefore explicitly encourage women to apply. Requirements: • MSc in neuroscience, biology, physics and a clear interest in animal behaviour. • Quantitative skills. Proficiency in at least one programming language is required (C, Python or Matlab) • Good communication and writing skills. Supervisors: Ahmed El Hady ahady(a)ab.mpg.de Einat Couzin-Fuchs einat.couzin(a)uni-konstanz.de For more information , please do not hesitate to contact me.

Dec. 2, 2021

Diversity in Research Papers Award - applications by 21.12

by Abigail Morrison

Dear colleagues, the Human Brain Project<https://secure-web.cisco.com/1W1yXA3r1eMXG2QECkXE7pE47kLRIgETwWjcqqDDu-0Bvs…> (HBP) launched the (DIRPA), inviting applications for the Best Diversity in Research Papers, i.e. publications that consider diversity traits such as sex, gender, age, ethnicity, etc. in their specific field of research such as neuroscience, AI or robotics. Differentiating variables has been recognised to be relevant from the level of stem cells to the reproduction of biases by AI applications. Considering sex/gender has become a mandatory requirement for Horizon Europe projects<https://secure-web.cisco.com/1N4suA7zlj2Htjj6Fi7aKdpAUd4iHisVvlrhWpFIHgjDbu…> (see also “Gendered Innovations” policy report<https://secure-web.cisco.com/1Z9Dobl_iN2xA4AcAe6cJuwwKTPhmwWVtRS87wuGclvzeA…>). The most outstanding papers will 1. be awarded with a certificate of honour. 2. be presented at the heart of a webinar to a large audience in a dedicated online event organised and promoted by the HBP<https://secure-web.cisco.com/1W1yXA3r1eMXG2QECkXE7pE47kLRIgETwWjcqqDDu-0Bvs…> and EBRAINS<https://secure-web.cisco.com/18-6-i2_g4ZweyCoaJtiyysPp45EhpsYRRnqKX35IoyD3n…>, where the authors will discuss their research related to diversity with Lutz Jäncke and further keynote speakers in April 2022. 3. be promoted with a news feature on the HBP and related Web Sites, as well as social media channels with several thousand followers. 4. especially early-stage researchers will receive a voucher for a HBP event of choice. Submission deadline: 21st December 2021 More information & submission: https://www.humanbrainproject.eu/en/about/gender-equality/measures-and-mate… _______________________________________________________ -- Prof. Dr. Abigail Morrison IAS-6 / INM-6 / SimLab Neuroscience Jülich Research Center & Computer Science 3 - Software Engineering RWTH Aachen http://www.fz-juelich.de/inm/inm-6 http://www.fz-juelich.de/ias/jsc/slns http://www.se-rwth.de Office: +49 2428 8097504 Fax # : +49 2461 61-9460 Pronouns: she/her ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Dec. 1, 2021

PhD position on electrical stimulation-induced changes in neuroplasticity at Inserm, Rennes, France

by Elif Köksal

*Title*: Neuro-inspired macroscale models of electrical stimulation-induced changes in neuroplasticity *Context*. Epilepsy refers to a neurological disorder that affects about 1% of the general population. Recent findings indicate that non-invasive brain transcranial current stimulation (tCS) is safe and of therapeutic promise in epilepsy. However, it is not yet indicated as a standard treatment due to major scientific limitations: unknown mechanisms of action, insufficient account for patient-specific factors, poor understanding of short- and long-term effects. The ambition of the GALVANI Project (ERC-SyG 2019; 2020-26) is to transform the care of a large fraction of patients living with drug-resistant epilepsies by solving a fundamental problem: to efficiently target and control large-scale epileptic brain networks with tCS-induced neuromodulatory weak electric fields ( https://www.galvani-lab.eu/) *Rationale*. Neuroplasticity refers to a wide ensemble of brain changes at cellular and network level that result from learning, practice, environmental influences, etc. In the normal brain, neuroplasticity is physiological process that allows for acquisition of new competences for instance. In the epileptic brain, neuroplasticity is a pathological process which alters the balance between excitation and inhibition giving rise to epileptic seizures. Neuroplastic changes may occur at different time scales (short and long) and may potentiate or, on the opposite, depress neuronal activity generated by brain circuits. Electrical stimulation (supra-threshold) and neuromodulation (sub-threshold) are two different methods that can be used to alter brain plasticity in order to lower hyperexcitability and subsequently decrease the occurrence of epileptiform events. *Objective*. This research focuses on neuromodulation. The objective of the proposed PhD position is to design neuroinspired macroscale models that will account for immediate (acute) and lasting (short- or long-term) effects of neuromodulatory weak electric fields, which remain elusive to some extent. *Methods*. After deep bibliographic review, biomathematical models to be developed will combine neurophysiological models of neuronal populations with mechanisms of action induced by weak electric fields on neuronal assemblies, typically on synaptic connectivity and firing rates. They will provide a unique framework to clarify and optimize the effects of dynamic E-fields induced by stimulation. They will be based on already-existing macroscale computational models which allow for simulation of epileptic activity (interictal spikes, ictal activity) generated by large-scale networks, as observed in human epilepsies. An issue to be solved is the translation from stimulation-induced short- and long-term effects at cellular level into average effects at population level. Optimization methods will be developed for identifying “therapeutic” neuromodulation parameters. Models will use the Neural Mass Model formalism (NMMs). They will be developed in Python. They will extend already-existing models at neural mass level. Strong background is available ( https://perso.univ-rennes1.fr/fabrice.wendling/) *Scientific domains*. Engineering (computational, biomedical); Physics (biophysics, electromagnetism); Biology (neuroscience); Medicine (neurology); Computer Science (computing in maths, engineering and Medicine) Scientific environment. GALVANI involves three partners: LTSI-Inserm (Rennes), AMU-APHM (Marseille) and Neuroelectrics (Barcelona). It is intended to develop the next generation of brain stimulation solutions. GALVANI can be viewed as a distributed lab (Rennes-Barcelona-Marseille) working under a common policy to ensure coherence of research and intense collaboration and cross-fertilization. Fellows will be co-supervised in a unique, shared environment with exposure to science, technology and clinical experience. *Candidate profile*. The research project is at the interface between biomathematics (neuro-inspired models), biophysics (electric field models), and neuroscience/neurology (epilepsy). The candidate will preferably have some background in dynamical systems, computational neuroscience/systems biology or in electrical engineering with experience in bio-signal processing and in biophysics. Knowledge in electrophysiology and/or EEG analysis would be an asset. The PhD fellow will join a multidisciplinary team including research scientists in biomedical engineering, neurophysiological modeling, bio-physics, signal processing, electrophysiology, neurology. *Contract*. The position will be opened* Feb. 1st, 2022*. The contract is for 3 years with possible extension (3 months). The salary will be defined according to Inserm rules regarding doctoral student remuneration. Location in the city of Rennes, France. LTSI-Inserm laboratory, University of Rennes. In addition, the PhD fellow will have the opportunity to perform visits and to actively collaborate with engineers, researchers and clinicians of the Marseille & Barcelona groups. *Contact *(please provide resume and cover letter) Fabrice Wendling (DR Inserm, LTSI, France) Email: fabrice.wendling(a)inserm.fr Pascal Benquet (Professeur, LTSI, France) Email: pascal.benquet(a)univ-rennes1.fr Elif Koksal-Ersoz (Post-doc fellow, LTSI, France) Email: elif.koksal-ersoz(a)inserm.fr

Dec. 1, 2021

Postdoc / Junior Scientist positions in Prague, Czech Republic

by Magda Pokorna

**1. Postdoctoral / Junior Scientist position in complex networks and information theory** is available to join the Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/> for the project: “Network modelling of complex systems: from correlation graphs to information hypergraphs“ funded by the Czech Science Foundation. More information and application at https://www.cs.cas.cz/job-offer/postdoc-junior-position-Hlinka5-2021/en** 2. Postdoctoral / Junior Scientist position in Multimodal Neuroimaging Machine Learning** is available to join the Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/> for the project: “Predicting functional outcome in schizophrenia from multimodal neuroimaging and clinical data“ funded by the Czech Health Research Council. More information and application at https://www.cs.cas.cz/job-offer/postdoc-junior-position-Hlinka6-2021/en ** ****** Do not hesitate to contact the principal investigator for informal inquiries concerning the position: Ing. Mgr. Jaroslav Hlinka, Ph.D., hlinka(a)cs.cas.cz. Jaroslav Hlinka Head of the Department of Complex Systems Institute of Computer Science Czech Academy of Sciences Pod Vodarenskou vezi 2 Prague 8, 182 07, Czech Republic Web: http://cs.cas.cz/hlinka

Dec. 1, 2021