- Comp-neuro - lists.cnsorg.org

2022 SPARC FAIR Codeathon (prize pool of US$50,000)

by Elisabetta Iavarone

Dear colleagues, we are looking for exciting projects which use SPARC data <https://sparc.science/data?type=dataset> and/or SPARC tools and resources <https://sparc.science/data?type=sparcPartners&developedBySparc=true&skip=0> for the peripheral nervous system in novel ways, particularly in enhancing, demonstrating, or measuring the findability, accessibility, interoperability, or reusability (FAIR) of the data. *Total prize pool of US$50,000* -- including cash prizes and manuscript publication fees. Project selection has begun, but it’s not too late to suggest a novel topic for consideration. The Codeathon will take place virtually, on 6-8 August. You can find more information on the SPARC codeathon page <https://sparc.science/help/2022-sparc-fair-codeathon>. Codeathon projects should result in code, tools, datasets, or other outputs which are open and freely available. Some coding experience is beneficial, but not necessary, as part of the project involves writing exhaustive documentation of your code and the aim of your project. Examples of projects from earlier codeathons are available on GitHub <https://github.com/SPARC-FAIR-Codeathon>, and here <https://docs.google.com/document/d/1OG3I0Oy1HivQNKOipNOZazFYCFVsSSn4Qe_EpSc…> you can find more ideas, such as: - Quantitative Analysis of Image Data - Visualizing experimental protocols - Create a short course on data science using Jupyter Notebook and the SPARC Portal <https://sparc.science/> - Embed o²S²PARC <https://docs.osparc.io/#/> modelling and simulation functionality within the SPARC Portal <https://sparc.science/> Participation in the codeathon is free and you only need access to your own computer and reliable internet connection to work with your team. We are looking forward to receiving your proposals. Best, Elisabetta (on behalf of the organizing committee)

July 1, 2022

Fully-funded PhD and PostDoc position (4 years) in Machine / Deep Learning in Translational Psychiatry, Charité - Universitätsmedizin Berlin, Germany

by Kerstin Ritter

Dear all, we offer one PostDoc position (4 years, 100%) and one PhD position (4 years, 75%) at Charité - Universitätsmedizin (Berlin, Germany) in Machine / Deep Learning in Translational Psychiatry in a newly established Research Unit 5187 "Precision Psychotherapy" (headed by Prof. Ulrike Lüken). Please see the job advertisements below. Please forward to potential candidates. Thanks, and best wishes, Kerstin (Ritter) ______________________________________________________________ Explainable Machine Learning / Deep Learning in Clinical Neuroimaging and Translational Psychiatry 1) PostDoc position (starting date: autumn 2022, 4 years; 100 %) at Charité - Universitätsmedizin (Berlin, Germany) At Charité - Universitätsmedizin Berlin and the Bernstein Center for Computational Neuroscience, we are looking for a motivated and highly qualified PostDoc for methods development at the intersection of explainable machine learning / deep learning and clinical neuroimaging / translational psychiatry. The position will be located in the research groups of Prof. Kerstin Ritter and Prof. John-Dylan Haynes at Charité Berlin. The main task will be to predict response to cognitive-behavioral psychotherapy in retrospective data and a prospective cohort of patients with internalizing disorders including depression and anxiety from a complex, multimodal data set comprising tabular data as well as imaging data (e.g., clinical data, smartphone data, EEG, structural and functional MRI data). An additional task will be to contribute to the organization and maintenance of the prospective cohort. This study will be one of several projects in the newly established Research Unit 5187 "Precision Psychotherapy" (headed by Prof. Ulrike Lüken). Requirements for the Postdoc: - Excellent master and PhD degree in relevant field (e.g. computer science, mathematics, physics, psychology, computational neuroscience or related). - Excellent methodological skills (esp. machine learning, deep learning, explainable AI, medical image analysis) - Excellent programming skills in python - Excellent writing and communication skills (in English) - Strong interest in neuroscientific and psychiatric research 2) PhD position (starting date: autumn 2022, 4 years; 75 %) at Charité - Universitätsmedizin (Berlin, Germany) At Charité - Universitätsmedizin Berlin and the Bernstein Center for Computational Neuroscience, we are looking for a motivated and highly qualified PhD student for analyzing structural and functional MRI data in patients with internalizing disorders (e.g., depression and anxiety) using machine learning methods. An additional task will be the acquisition of fMRI data together with other PhD students in the newly established Research Unit 5187 "Precision Psychotherapy" (headed by Prof. Ulrike Lüken). The PhD student will be supervised by Prof. Kerstin Ritter, Prof. Ulrike Lüken and Prof. Norbert Kathmann. Requirements for the PhD student: - Excellent master in relevant field (e.g. computer science, mathematics, physics, psychology, computational neuroscience or related). - Very good methodological skills (esp. machine learning, deep learning, statistics, neuroimaging) - Very good programming skills in python - Excellent writing and communication skills (in English and German) - Strong interest in neuroscientific and psychiatric research Please send your application (motivation+CV+references) in one pdf-file (in English or German) asap to: Prof. Dr. rer. nat. Kerstin Ritter Charité - Universitätsmedizin Berlin Department of Psychiatry and Psychotherapy Bernstein Center for Computational Neuroscience Sauerbruchweg 4, Charitéplatz 1, 10117 Berlin E-Mail: kerstin.ritter(a)charite.de Webpage: https://psychiatrie-psychotherapie.charite.de/en/research/translation_and_n…

July 1, 2022

NEURON School on basic Computational Neuroscience 12-16 September 2022 ITALY

by Sergio Solinas

**Apologies for cross-posting** [All details about this school can be found online at The NEURON School < https://www.neuronschool.org/>] The organisers are excited to announce the third edition of The NEURON School on Computational Neuroscience. This *one-week* school will introduce the basic use of the simulation environment NEURON and related software to build brain models from experiments to their applications. - The school will provide basic notions on experimental methods to extract and process morphological and electrophysiological data targeting their use to build computational models of single neurons and neuronal networks. - The school will cover how these models can be constructed based on the principles of biological tissue electrophysiology. We welcome applications from full graduate, PhD students, and PostDocs in a variety of fields from biology, neurobiology and psychology, to physics, engineering, and mathematics, and industry professionals with a relevant background. Applicants are expected to have a good background in their discipline, an interest in neuroscience, and some knowledge (even basic) of computer programming. We will soon post updates and a flyer about the school organisation. *Format*: Morning tutorials will be complemented with Afternoon coding sessions and Evening discussions promoted by presentations of Senior Scientists. *Date and Location:* September 12th to September 16st, 2020 at the Pula Research Centre < https://www.sardegnaricerche.it/index.php?xsl=376&s=13&v=9&c=3874&nc=1> within the Science and Technology Park of Sardinia, Cagliari - Sardinia (ITALY). Application Deadline: 15 August 2022 *Applications*: Please visit https://www.neuronschool.org/ where you can find more information regarding costs, travel, and lodging. If you have any questions about the school or the application process, please contact smgsolinas(a)uniss.it or enrico(a)uniss.it We look forward to your registration and to welcoming you to the Pula Research Centre!

June 30, 2022

[JOBS] PhD @ Italian Institute of Technology, Ferrara

by Alessandro D'Ausilio

PHD PROGRAM in TRANSLATIONAL NEUROSCIENCES AND NEUROTECHNOLOGIES The Center for Translational Neurophysiology of Speech and Communication (CTNSC) @ Italian Institute of Technology (IIT), jointly with the University of Ferrara, are opening up to 8 PhD positions starting in November 1st, 2022. Research areas: - Improving performance and biocompatibility of electrode arrays for brain-computer interfaces - Organic neuroelectronics for multimodal recordings and stimulation of the brain in vivo - Hardware and software development for innovative exploration of brain signals - Machine learning applications to multimodal brain and speech signals - Investigation of sensorimotor functions in animal models - Cortical recordings in human patients during awake Neurosurgery - Human non-invasive neurophysiology of speech and sensorimotor communication by means of TMS, EEG, EMG and MoCap Who: physicists, computer scientists, biomedical/electrical engineers, biologists, biotechnologist, medical doctors and experimental psychologists eager to work in an international and multidisciplinary team. Where: The CTNSC (https://www.iit.it/it/ctnsc-unife <https://www.iit.it/it/ctnsc-unife>) is hosted by the University of Ferrara (UNIFE) in a prestigious historical building in the city center. Ferrara is a well connected renaissance city (30-min to Bologna, 40-min to Padua, 60-min to Venice; 2 nearby international airports), bustling with students (https://whc.unesco.org/en/list/733 <https://whc.unesco.org/en/list/733>). General INFO: http://www.unife.it/studenti/dottorato/it/corsi/riforma/neuroscience <http://www.unife.it/studenti/dottorato/it/corsi/riforma/neuroscience> Application INFO: http://www.unife.it/studenti/dottorato/concorsi/selection <http://www.unife.it/studenti/dottorato/concorsi/selection> Application website: https://pica.cineca.it/unife/dottorati-38-ntn/ <https://pica.cineca.it/unife/dottorati-38-ntn/> DEADLINE: July 25rd, 2022

June 30, 2022

Workshop on State of the Art Methods for Brain Data Analysis

by Dimitris Pinotsis

State of the Art Methods for Brain Data Analysis- A workshop for computational, theoretical and cognitive neuroscientists taking place on July 6 at City— Universıty of London This hybrid workshop will discuss the state of the art methods in brain imaging and how they inform our understanding of the neural basis of behaviour and cognition. It will be of interest to computational and cognitive neuroscientists who are keen on brain imaging, computational psychiatry and network-level dynamics. Speakers: - John Ashburner, UCL - Aldo Faisal, Imperial - Gene Fridman, Johns Hopkins - Alan Jasanoff, MIT - Marcus Kaiser, Nottingham - Mark Woolrich, Oxford Hybrid format (f2f and online) July 6th, 2022 09:50 - 17:00 B200 Lecture Theatre, University Building, 2nd Floor, City, University of London Read more here: About | Brain Data Analysis (braindatanalysis.wixsite.com) Registration is free. To register, please fill in this form: . For any questions, please email braindatanalysis(a)gmail.com

June 28, 2022

2022 Western-Fields School in Networks and Neuroscience

by Lyle Muller

Applications are invited for a one-week school at the interface of mathematics and neuroscience. With similar scope as the 2021 joint seminar series<http://www.fields.utoronto.ca/activities/21-22/western-fields>, the Western-Fields Summer School in Networks and Neuroscience<https://uwo.ca/academy/themes/neural_networks/2022_western_fields_school.ht…> will bring together advanced undergraduate students, graduate students, and postdocs for a week of training in methods for networks, dynamics, learning, and modeling biological neural networks. Lectures will cover graph theory, network dynamics, advanced algebra, and machine learning. Students will receive intensive training ranging from an introduction to advanced methods in these fields. This summer school will be held September 19-23 on the campus of Western University (London, Ontario), with a closing session at the Fields Institute (Toronto, Ontario). Applications should consist of CV and one-page statement of interest, submitted as a single PDF file to Lyle Muller (lmuller2(a)uwo.ca<mailto:lmuller2@uwo.ca>) and Ján Mináč (minac(a)uwo.ca<mailto:minac@uwo.ca>). Review of applications will begin on 6 July 2022. Our team is committed to fostering diversity in mathematics and neuroscience, and a goal of this summer school is to encourage diverse candidates with quantitative training to consider problems in this growing field. Any interested applicants can write to the teaching team with questions about the program. -- Lyle Muller http://mullerlab.ca<http://mullerlab.ca/>

June 27, 2022

2022 Western Academy for Advanced Research Postdoctoral Competition

by Lyle Muller

The Western Academy for Advanced Research<https://uwo.ca/academy/index.html> is launching a competition for highly motivated postdoctoral researchers<https://uwo.ca/academy/themes/neural_networks/2022_postdoctoral_competition…> at the interface of mathematical modeling and neuroscience. Successful candidates will join a new, research-intensive program at Western University. The Western Academy’s opening Theme will develop connections between mathematics and neuroscience, leveraging mathematical approaches to answer open questions in neuroscience. Motivated postdoctoral candidates are encouraged to submit application materials, including a CV, short research statement, and contact information for three academic references, to Lyle Muller (lmuller2(a)uwo.ca<mailto:lmuller2@uwo.ca>) and Ján Mináč (minac(a)uwo.ca<mailto:minac@uwo.ca>). Postdocs will receive competitive stipends and support for their academic careers. Review of applications will begin 15 July 2022. Both our group and the University are deeply committed to fostering diversity in the sciences. Applications from underrepresented groups are strongly encouraged, and any interested applicants can write the PIs directly with questions about the research environment. -- Lyle Muller http://mullerlab.ca

June 27, 2022

Fully-funded PhD project on networks in Mark Humphries’ lab, University of Nottingham (Oct 2022 start)

by Mark Humphries

A fully-funded 3.5 year PhD project is available in the Mark Humphries’ lab at the University of Nottingham, UK. Broad classes of network models, like small-world networks and scale-free networks, have taught us much about the world. But we suspect a major class of networks has been missed. This project will introduce and explore a new class of model weighted networks, “divergent” networks, in which the structure described by the links and their weights do not match. Most theoretical work on weighted networks assumes that they do, so little is known about the properties of these divergent networks. We will close that gap by quantifying the existence and extent of divergence in a range of real-world networks, including brain connectomes at both single neuron and inter-area level; by creating generative models for these networks; and by exploring how divergence alters a network’s dynamics across a range of dynamical systems implemented on the nodes, including neural models. The student will be joining the Humphries lab (https://www.humphries-lab.org/) who draw on network theory and dynamical systems approaches to understand neural coding and computations. They will also be co-supervised by Prof Stephen Coombes (School of Maths), an expert in dynamics on networks. Suggested reading: Humphries, M. D., Caballero, J. A.*, Evans, M.*, Maggi, S.* & Singh, A.* (2021) Spectral estimation for detecting low-dimensional structure in networks using arbitrary null models. PLoS ONE, 16(7): e0254057. Enquiries: mark.humphries(a)nottingham.ac.uk<mailto:mark.humphries@nottingham.ac.uk> (send a CV with queries please) Application deadline: July 29th 2022 Further details, and how to apply: https://www.findaphd.com/phds/project/divergent-networks-a-new-class-of-com… Funding information: EPSRC DTP studentship, 3.5 years duration. Start: October 2022 Studentship will pay Home (UK) University tuition fees (minimum £4,596 per year) and a minimum stipend of £16,062 per year for your living costs. International students are welcome to apply, but note the studentship does not cover international tuition fees (currently £26,000 per year). Professor Mark Humphries | Professor of Computational Neuroscience My book "The Spike: An Epic Journey Through the Brain in 2.1 Seconds" is out now in hardback, ebook, and audiobook! https://press.princeton.edu/books/hardcover/9780691195889/the-spike Lab: humphries-lab.org<https://www.humphries-lab.org/> Twitter: @markdhumphries Public blog: https://medium.com/the-spike This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

June 26, 2022

Tutorial and Workshop on Neuron-Glial Interactions at the CNS*2022 (Melbourne, Australia)

by De Pitta, Maurizio

Dear colleagues, Please mark them on your calendar. Share and disseminate into your networks. We are organizing a Tutorial and a Workshop on Computational Methods and Models of Neuron-Glial interactions, at the forthcoming Annual Meeting of the Organization of Computational Neurosciences (CNS*2022), in Melbourne, VIC, Australia. Both events will be in person. ***Tutorial on Models of Neuron-Glial Interactions*** Melbourne Convention and Exposition Center (MCEC) July 16, 2022; 9AM -- 6.15PM Session 1 (morning): Oligodendrocyte modeling Daniel Park, Afroditi Talidou, Jeremie Lefebvre (University of Ottawa, Canada) Session 2 (morning): Astrocytic Calcium modeling Hugues Berry (INRIA Lyon, France) Session 3 (afternoon): Tripartite synapses and neuron-glial networks Maurizio De Pitta (Krembil Research Institute, Canada) Session 4 (afternoon): Ionostasis at the tripartite synapses Marinus Toman, Liam McDaid (University of Ulster, Northern Ireland, UK) Please visit the Tutorial Website for more info: https://sites.google.com/view/cns2022-tutorial-on-modeling-n/home ***Workshop on Emerging Perspectives and Models on Neuron-Glial Interactions*** Melbourne Convention and Exposition Center (MCEC) July 19, 2022; 2PM -- 6PM July 20, 2022; 8:30AM -- 7:30PM Day 1: Hugues Berry, INRIA Lyon, France Corrado Cali, University of Turin, Italy David Gonsalvez, Monash University, Australia Leonid Savtchenko, University College London, The United Kingdom Tanya Tchumatchenko, University of Mainz Medical Center, Germany Day 2: Maurizio De Pittà, Krembil Research Institute, Canada Adi Doron, The Hebrew University of Jerusalem, Israel Jeremie Lefebvre, University of Ottawa, Canada Liam McDaid, Ulster University, Northern Ireland, The United Kingdom Ciaran Murphy-Royal, Université de Montréal, Canada Marlene Hao, The University of Melbourne, Australia Daniela Pietrobon, University of Padua, Italy Christine R. Rose, Heinrich Heine University, Germany Annalisa Scimemi, State University of New York at Albany, USA Please visit the Workshop Website for more info: https://sites.google.com/view/cns22-ngi-iworkshop/home To attend the Tutorial and the Workshop, Registration through the CNS*2022 is required: https://www.cnsorg.org/cns-2022-registration-fees We are looking forward to seeing you in Melbourne. Thank you for your consideration. Maurizio ----- Maurizio DE PITTA Principal Investigator Neuron-Glia Interactions Lab (NGILab) Krembil Research Institute, 4KD-509 60 Leonard Ave, Toronto, ON M5T 0S8, CA +1.416.603.5800 ext. 3290 This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization. If you feel you have received an email from UHN of a commercial nature and would like to be removed from the sender's mailing list please do one of the following: (1) Follow any unsubscribe process the sender has included in their email (2) Where no unsubscribe process has been included, reply to the sender and type "unsubscribe" in the subject line. If you require additional information please go to our UHN Newsletters and Mailing Lists page. Please note that we are unable to automatically unsubscribe individuals from all UHN mailing lists. Patient Consent for Email: UHN patients may provide their consent to communicate with UHN about their care using email. All electronic communication carries some risk. Please visit our website here<https://www.uhn.ca/PatientsFamilies/Patient_Safety_Advocacy/Privacy/Documen…> to learn about the risks of electronic communication and how to protect your privacy. You may withdraw your consent to receive emails from UHN at any time. Please contact your care provider, if you do not wish to receive emails from UHN.

June 24, 2022

Reminder: Free online CNS*2022 satellite tutorials: June 27--July 1

by Ankur Sinha

Dear all, Apologies for the cross-posts. A final reminder of next week's CNS*2022 free online satellite tutorials (from June 27--July 1): https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… Free registration remains open at: https://framaforms.org/incfocns-software-wg-cns2022-satellite-tutorials-reg… To prevent spam/zoom crashing, links to zoom meetings for the tutorial sessions will be limited to registrants only. Therefore, while registration is free, it is required. The satellite tutorials feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - NeuroLib - NeuroML - NEURON - OSBv2 - RateML Please spread the word, and we look forward to seeing you there! -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

June 23, 2022