November 2020 - Comp-neuro - lists.cnsorg.org

Free Online Seminar: How to build your own Connectome?

by Markus Butz-Ostendorf

Dear List, My apologies for cross-postings first of all! I would like to draw your attention to our second online seminar on Connectomics. We have invited our clinical neuroimaging specialist Dr Yong Li from Biomax Brain Science to demonstrate how brain tumors change the human Connectome and how the Connectome heals after tumor surgery. Abstract at the end of this message. The seminar takes place online on Tue, 10 Nov 2020 at 3pm (CET). Participation is free of charge but registration is kindly requested via this link https://www.biomax.com/webinar Explore NICARA yourself by registering a free demo account at https://ssl.biomax.de/nicara/ Kind regards, Markus == *Abstract* Brain damage such as tumors, traumatic brain injury or stroke alter the characteristics of the broader connectome—the map of all neural connections in the brain. A hot topic in ongoing research using the connectome approach is how brain rewiring can compensate for lesion-induced cognitive deficits before and after intervention. The site of a lesion within the connectome is critical. Damage of a node that acts e.g. as an integrator hub of several subnetworks is significantly more detrimental to cognitive functions than a damaged node with low connectivity or existing by-passes. Understanding brain rewiring in response to lesions is the major focus of clinical as well as computational neuroscience projects (such as The Virtual Brain) to pave the way for personalized medicine in neurology and related fields. In this online seminar we will focus on brain tumors and explore their effects on the connectome using NICARA™. A particular image processing pipeline in NICARA, employing the best available open-source tools for image preprocessing and probabilistic fiber tracking, enabled us to automatically extract full brain tractography based structural connectome data from DTI raw images. Besides the pipeline, we will discuss quality control mechanisms especially designed for the assessment of large cohorts. As an example, data set we used the Brain Tumor Connectomics Data (Aerts H et al. Modeling Brain Dynamics in Brain Tumor Patients Using the Virtual Brain. eNeuro. 2018 Jun 4;5(3): ENEURO.0083-18.2018.) and assessed alterations in major white matter fiber tracts before and after surgery. For quantification, provided not only the abstract presentation of digitalized connectome networks in MNI space by a 3D lattice graphs but also offered fiber density maps directly in the patient’s native T1w for a precise judgement of fiber pathway density distribution in the vicinity of, and remote to, a tumor. Our clinical neuroimaging specialist Dr. Yong Li will further show how he uses NICARA to explore, manage and compare extracted connectome networks for group comparisons, individual patient-matched controls comparisons and longitudinal assessments. NICARA is a novel neuroimaging tool created by clinical neuroimaging scientists for clinical and translational neuroscience users. A technical introduction by product manager Dr. Markus Butz-Ostendorf at the end of the seminar on how NICARA stores and retrieves connectome information using of knowledge models will complement the scientific presentation. The seminar will take place on November 10, 2020 at 3:00 p.m. (CET) and will last about 45 minutes. Make use of this opportunity and register today at www.biomax.com/webinar. Next seminar for Pharmacologists : 1/12/2020, 3:00 pm To register, please go to https://www.biomax.com/webinar and request your access data via the webinar page. We are looking forward to meeting you. -- Dr. rer. nat. Markus Butz-Ostendorf Innovation Manager Brain Science Senior Product Manager Biomax Informatics AG Robert-Koch-Str. 2, 82152 Planegg, Germany Registergericht: Amtsgericht München, HRB 134442 Vorstand: Dr. Klaus Heumann Vorsitzender des Aufsichtsrates: Prof. Dr. Hans-Werner Mewes Tel: +49 89 895574-862 Fax: +49 89 895574-825 Email:markus.butz-ostendorf@biomax.com Website:http://www.biomax.com PGP:https://ssl.biomax.de/pgp/

Nov. 6, 2020

COSYNE 2021: Abstract submission closes soon; Registration info

by Tomas Hromadka

==================================================== Computational and Systems Neuroscience 2021 (Cosyne) MAIN MEETING ONLINE 24 - 26 February 2021 www.cosyne.org ==================================================== The Cosyne abstract deadline is just one week away! Abstracts are due November 12, 2020 by 11.59pm PST. This year, because of the generous support of donors, we will be able to make registration low- or no-cost for a large number of attendees. Registration will open after final decisions are made on abstracts in January 2021. Registration rates will be $25 for students and postdocs, $100 for all other academics, and $150 for corporate attendees. We will have a fee waiver open for >1000 registrants. We will share additional details as support is finalized in the next few weeks. If you would like help revising your abstract before the deadline, or helping provide feedback to others, please consider joining the Cosyne Mentoring Forum! Rainer Engelken and Stephanie Palmer are organizing a google group to offer positive, constructive critiques of abstracts, along with "pro tips" for conveying the ideas and impact in your work effectively. Please sign up to review abstracts and submit your own for feedback. You can email sepalmer [at] uchicago.edu directly and also join the Cosyne mentoring group. Visit Cosyne.org -> Mailing lists for details on how to join the group. ---------------------------------------------------- COSYNE ---------------------------------------------------- The annual Cosyne meeting provides an inclusive forum for the exchange of empirical and theoretical approaches to problems in systems neuroscience, in order to understand how neural systems function. Cosyne topics include but are not limited to: neural basis of behavior, sensory and motor systems, circuitry, learning, neural coding, natural scene statistics, dendritic computation, neural basis of persistent activity, nonlinear receptive field mapping, representations of time and sequence, reward systems, decision-making, synaptic plasticity, map formation and plasticity, population coding, attention, and computation with spiking networks. Cosyne 2021 will take place online, February 24 - 26, 2021. The goal of this year's meeting is to promote early stage investigators. Therefore, there are no invited talks from established researchers. The format will include featured contributed talks chosen from submitted abstracts, and interactive poster-like presentations (short recorded presentation + live interactions). More details to follow. All abstract submissions will be reviewed as in previous years, but reviewing will be fully double blind. When preparing an abstract, authors should be aware that not all abstracts can be accepted for the meeting. Abstracts will be selected based on the clarity with which they convey the substance, significance, and originality of the work to be presented. ---------------------------------------------------- COSYNE 2021 TUTORIAL ---------------------------------------------------- Cosyne 2021 main meeting will be preceded by an online Cosyne Tutorial Session led by Kanaka Rajan (Icahn School of Medicine at Mount Sinai) on 23 February 2021. More details will be posted on www.cosyne.org. ORGANIZING COMMITTEE General & Program Chairs: Anne-Marie Oswald (U Pittsburgh) and Srdjan Ostojic (Ecole Normale Superieure Paris) Diversity Chairs: Eva Dyer (Georgia Tech, Emory) and Eric Shea-Brown (U Washington) Publicity Chair: Adam Calhoun (Princeton) Tutorial Chair: Il Memming Park (Stony Brook) Development Chair: Michael Long (NYU) EXECUTIVE COMMITTEE Stephanie Palmer (U Chicago) Zachary Mainen (Champalimaud) Alexandre Pouget (U Geneva) Anthony Zador (CSHL) PROGRAM COMMITTEE Athena Akrami (UCL) Demba Ba (Harvard) Omri Barak (Technion) Brice Bathellier (Paris) Yoram Burak (Hebrew University) Christine Constantinople (NYU) Saskia De Vries (Allen Institute) Victor de Lafuente (UNAM Mexico) Jan Drugowitsch (Harvard) Tatiana Engel (CSHL) Annegret Falkner (Princeton) Kevin Franks (Duke) Tim Hanks (UC Davis) Ann Hermundstad (Janelia) Andrew Leifer (Princeton) Sukbin Lim (Shanghai) Scott Linderman (Stanford) Mackenzie Mathis (EPFL Lausanne) Ida Momennejad (Microsoft) Cris Niell (U Oregon) Il Memming Park (Stony Brook) Adrien Peyrache (McGill Montreal) Kanaka Rajan (Icahn School of Medicine at Mount Sinai) Robert Rosenbaum (Notre Dame) Christina Savin (NYU) Marshal Shuler (Johns Hopkins) Daniela Vallentin (Max Planck Munich) CONTACT meeting [at] cosyne.org COSYNE MAILING LISTS Please consider adding yourself to Cosyne mailing lists (groups) to receive email updates with various Cosyne-related information and join in helpful discussions. See Cosyne.org -> Mailing lists for details.

Nov. 5, 2020

Grant For Equipping Electrophysiology Labs

by Maryam

Dear researchers, We are happy to announce that in order to accelerate neuroscience researches, ScienceBeam, a designer and manufacturer of neuroscience applications including EEG/ERP, QEEG, Neuro-Biofeedback and animal electrophysiology systems, is providing limited number of grants (30% - 70%) for equipping the neuroscience/electrophysiology laboratories to any young researcher with a well-defined research proposal. We particularly want to encourage outstanding candidates to apply for the ScienceBeam grant. We are also very keen to invite graduate students, who are towards the end of their Ph.D. and desire to return to their country to promote research in the field of Basic and Clinical Neuroscience. This Grant is offered for the below equipment: ➢ Neuro-biofeedback device ➢ Animal electrophysiology system ➢ EEG/QEEG/ERP acquisition system Consider the below terms and conditions: • Researches related to diagnosis and treatment of sensorimotor disorders (Multiple Sclerosis (MS), Alzheimer’s disease, and Parkinson) • Researches related to diagnosis and treatment of psychological and cognitive disorders. • Researches related to diagnosis and treatment of mental and nervous rehabilitation. To apply for any above grants please consider the following points: • Candidates should have a Ph.D. in neuroscience, physiology, pharmacology, psychology, medical engineering, and any related area. • Interested candidates must send an email request to grant(a)sciencebeam.com including their resumes and research proposal. • Candidates should submit a cover letter, a curriculum vitae, a list of publications, and a clear research proposal describing her/his research plan for two next year’s describing why they need our products. • Young candidates should arrange for two letters of recommendation sent on their behalf to grant(a)sciencebeam.com • All materials must be submitted to grant(a)sciencebeam.com until December 1st, 2020. For more information visit the link below: https://sciencebeam.com/mid-autumn-festival/ And submit your resume and research proposals to: grant(a)sciencebeam.com

Nov. 5, 2020

Virtual Training Webinar: Introduction to the Neuroscience Gateway Using NEURON and EEGLAB; November 20, 2020; 9:30 AM - 12:30 PM US Pacific Time

by Majumdar, Amitava

Date of Neuroscience Gateway training webinar: Friday, November 20, 2020 Time: 9:30 AM - 12:30 PM US Pacific Time Registration is free (but total registration is limited): https://www.sdsc.edu/event_items/202011_NSGwebinar.html The Neuroscience Gateway (NSG<https://www.nsgportal.org/index.html>) enables large scale modeling and data processing research in neuroscience. NSG provides easy to use web portal based and programmatic access to supercomputing and high throughput computing resources. NSG is free and open to researchers and students. NSG provides about 20 widely used neuroscience software<https://www.nsgportal.org/software.html> for modeling, simulation, data processing, data analysis and machine learning optimally installed on supercomputing and high throughput computing resources. Neuroscientists who plan to use NSG for their research, irrespective of which of the NSG-provided neuroscience software they may use, will find this webinar useful. This webinar will provide training on how to use the NSG and its various features within the context of two widely used neuroscience software for modeling and data processing - NEURON and EEGLAB. The NEURON<https://neuron.yale.edu/neuron/> simulation environment is used by researchers and students worldwide for building and using computational models of neurons and networks of neurons. EEGLAB<https://sccn.ucsd.edu/eeglab/index.php> is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics. We will also talk about a new supercomputer called Expanse<https://www.sdsc.edu/services/hpc/expanse/> that is becoming available to NSG for running these software. NSG is funded by the US National Science Foundation and National Institutes of Health. Agenda (listed in Pacific Time) * 9:30am - 9:50am: Introduction to NSG * Amit Majumdar, Kenneth Yoshimoto, Subhashini Sivagnanam, San Diego Supercomputer Center, University of California San Diego * 9:50am - 10:10am: Demo of using NSG - via the portal and the programmatic REST access * Subhashini Sivagnanam, San Diego Supercomputer Center, University of California San Diego * 10:10am - 10:35am: Introduction to NEURON * Ted Carnevale, Department of Neurobiology, Yale University * 10:35am - 10:55am: Demo of using NSG for NEURON * Ted Carnevale, Department of Neurobiology, Yale University * 10:55am - 11:10am: Break * 11:10am - 11:30am: Introduction to EEGLAB * Arnaud Delorme, Swartz Center for Computational Neuroscience, University of California San Diego * 11:30am - 12:10pm: Demo of using NSG for EEGLAB * Arnaud Delorme, Swartz Center for Computational Neuroscience, University of California San Diego * 12:10pm - 12:30pm: Q&A For questions, please email nsghelp(a)sdsc.edu -Amit Majumdar NSG Team San Diego Supercomputer Center University of California San Diego

Nov. 4, 2020

Two year postdoctoral position in Computational Neuroscience at the European Neuroscience Institute

by Jaramillo, Jorge Hernan Hoyos

Dear Colleagues, The Distributed Neural Dynamics and Control group at the European Neuroscience Institute (ENI) in Göttingen, Germany invites applications for a two year postdoctoral position focused on the simulation of subcortical and cortical dynamics in the context of cognitive function and clinical applications. A quantitative background and programming skills are required (e.g., PhD in Computational Neuroscience, Physics, Engineering), while experience with dynamical systems and previous exposure to neurobiology are preferred. Details of the position and application instructions can be found here: https://www.umg.eu/karriere/stellenangebote/stellenanzeigen-detail/?jobId=3… Application deadline: 15 Nov, 2020 Start: January 2021. Women are especially encouraged to apply. Applicants with disabilities and equal qualifications will be given preferential treatment. For any questions about the position, please contact Jorge Jaramillo ( j.jaramillo(a)eni-g.de ). Jorge Jaramillo ENI Group Leader: Distributed Neural Dynamics and Control http://www.eni-g.de/groups/distributed-neural-dynamics

Nov. 4, 2020

Postdoctoral Research Assistant in Learning Algorithms for Neurmorphic Computing, Stralsund, Germany

by André Grüning

In the lab of Prof Gruening and within the EU-funded research project "The Human Brain Project" we are offering a 24months fixed-term postdoctoral post, available immediately. ‍The formal job ad can be found at https://www.hochschule-stralsund.de/host/aktuelles/stellenangebote/ (in German only), but feel free to contact me informally in person and in English at <mailto:andre.gruening@hochschule-stralsund.de>. ‍Welcome to the University of Applied Sciences Stralsund! With our campus on the shores of the Baltic Sea, we deliver industrial related studies with excellent job prospects to about 2300 students. Life on our campus is characterised by excellent facilities for both teaching and research and flat hierarchies. The historical centre of the UNESCO world heritage town of Stralsund is within easy reach on foot; maritime water sports, nature and the island of Rugia at our doorstep stand for the highest quality of life. As a certified family-friendly institution we embrace modern life and a proper work-life balance. We are looking forward to meeting people who are keen to strengthen our research team and are advertising the following fixed-term post, subject to confirmation of funding: **Research Assistant (f/m/d) in the EU-funded research project “The Human Brain Project”** The post is available immediately for 24 months (full-time) for a postdoctoral candidate. You will be working in the area of artificial intelligence based on neuromorphic hardware. Neuromorphic hardware is a modern and active area of research with the aim to design devices for artificial intelligence that utilise the spike-based operation of biological nervous systems. The energy consumption of such systems for example promises to be an order of magnitude less than classical AI systems. Neuromorphic systems are being developed within academic research as well as in industry. The work will be carried out in close cooperation with research groups across Europe that are partners in the Human Brain Project, for example groups at the Universities of Heidelberg, Bern or Manchester. **Your job responsibilities include the following:** - Development, implementation and evaluation of learning rules for artificial spiking neural networks with the aim to realise deep learning on neuromorphic hardware. - Contribution to and cooperation within the international framework of the EU/H2020 Flagship project “The Human Brain Project”, see <https://www.humanbrainproject.eu/> in the area described above. - Participation in project management and reporting. **We expect from you:** - A PhD in a relevant area, for example computer science, mathematics, physics, cognitive science and neuroscience or engineering. - Programming experience, for example Python, C, C++. Experience with embedded systems is a plus. - Experience within the area of artificial neural networks. - Keen interest to familiarise yourself with the neuroscientific foundations of the project. - Experience with Unix-like operating systems and tool chains. - Experience in the write up of scientific reports and publications. Experience with LaTeX is a plus. - Experience with presenting research results. - Solid mathematical expertise. - A conscientious, independent and self-motivated attitude towards work. **We offer:** - A diverse, interesting and challenging job at an innovative, modern and family friendly institution in the lively world-heritage and Hanseatic town of Stralsund. - A work contract subject to the collective labour agreement of the public service of the German federal states (TV-L). - Remuneration up to pay grade 13 subject to personal and collective qualifying conditions. - 40 hrs/week; part-time and flexible work is possible. The University of Applied Science Stralsund is keen to increase the proportion of female employees in all areas where they are underrepresented. We therefore expressly invite qualified women to apply. As a certified family-friendly institution we support actions to reconcile family and job. Childcare can be arranged for a potential future interview. At an equal level of professional aptitude, applicants with recognised disabilities or equivalent (please provide evidence) will be preferred. For details of the job description, please contact Prof André Grüning (E-Mail: <mailto:andre.gruening@hochschule-stralsund.de>). According to §68 Abs 3 PersVG M-V, the Employee Committee (Personalrat) gets involved into HR matters for research staff only on the candidate’s request. If desired, please include such request in free form within your application documents. Please send your job application with all relevant documents in a single pdf file to <mailto:bewerbungpersonal@hochschule-stralsund.de> or by mail to Hochschule Stralsund Vertrauliche Personalangelegenheit Dezernat Personal, Haushalt und Controlling Zur Schwedenschanze 15 18435 Stralsund on or before the **deadline of 15.11.2020**. Thereafter applications will be reviewed until the post is filled. The protection of your personal data is very important to us. We will therefore collect, process and utilise any data arising in the application process only in line with the applicable data protection regulations. As application documents cannot be returned, please submit copies only. The University of Applied Sciences Stralsund does not cover any application expenses, including those arising for a potential interview. -- Prof. Dr. André Grüning -- Mathematik und Künstliche Intelligenz Fakultät Elektrotechnik und Informatik Hochschule Stralsund -- Mathematics and Computational Intelligence Faculty of Electrical Engineering and Computer Science University of Applied Sciences Stralsund -- 18435 Stralsund Deutschland/Germany

Nov. 4, 2020

NEURON Virtual Course deadline approaching

by Ted Carnevale

*What:* The one-day NEURON course presented as a series of short webinars. *When:* The webinars will run from 1 PM to 3 PM New York time on Monday and Tuesday, Nov. 16 and 17, and on Monday and Tuesday, Nov. 23 and 24, 2020 *Speakers:* Ted Carnevale and Robert McDougal Registration is on a first-come, first-serve basis, and the deadline is Friday, November 13, 2020 at 5 PM New York time. There is no fee, but *total registration will be limited to 40 individuals* in order to be most responsive to participants' questions. For more information and a link to the application form: https://neuron.yale.edu/neuron/static/courses/nrn2020/nrn2020.html

Nov. 4, 2020

Interdisciplinary Neuroscience PhD programme, Tübingen

by Peter Dayan

The Max Planck Institute for Biological Cybernetics, the Hertie Institute for Clinical Brain Research and the University of Tübingen invite students from all over the world to apply for their interdisciplinary 5-year PhD program leading to a PhD in Neuroscience. Full funding will be available for top-ranked applicants. We are seeking talented, curious and open-minded young scientists with strong backgrounds in neuroscience, biomedical sciences, computational science, applied mathematics, statistics, artificial intelligence, or engineering. Successful candidates will possess a burning aspiration to shape the future of neuroscience and the ability to thrive in a fast-paced, interdisciplinary, environment. The application deadline is 30th November 2020. Please visit: https://www.kyb.tuebingen.mpg.de/imprs-mmfd for more details and information about applying. The PhD program is a collaboration between the Max Planck Institute for Biological Cybernetics, the Hertie Institute for Clinical Brain Research and the University of Tübingen. It is closely affiliated with the renowned Graduate Training Centre of Neuroscience, the centerpiece of neuroscience training in Tübingen. Students (who should have been awarded a Bachelor's degree by September 2021) will receive a broad interdisciplinary training in neuroscience, including expert teaching by international renowned scientists and individual and intensive mentoring. Potential research topics cover a variety of fields in systems neuroscience, cognitive and behavioral neuroscience, computational neuroscience, translational and clinical neuroscience as well as cellular and molecular neuroscience. Teaching and research are conducted in English.

Nov. 3, 2020

Deadline extended to Nov. 15th Postdoctoral position for the development of acquisition, storage and processing pipelines for reproducible science building on the BIDS standard.

by Jochem Rieger

Dear colleagues, We have an open post-doc level position for 3+2 years at the Neuroimaging Unit of Uni Oldenburg for the development of tools and infrastructure for open data data and reproducible science based on the BIDS standard. The position complemented by a full time technician position for support. The announcement is below. Please contact me if you have questions. We are looking forward to applications, Jochem The Neuroimaging Unit at the School of Medicine and Health Sciences of the Carl von Ossietzky Universität Oldenburg is seeking to fill the position of a *Postdoctoral Research Associate m/f/d *(Salary level E13 TVL, 100%) *for the development of acquisition, storage and processing pipelines for reproducible science building on the BIDS standard.* The position is embedded in a DFG Core Facility grant and is available*as soon as possible*for a duration of three years (with the possibility to extend another two years after successful project evaluation). The position is suitable for part-time work. In a newly funded project we aim to implement data storage and processing pipelines for reproducible science building on the BIDS standard. The Neuroimaging Unit hosts a state of the art MEG (Elekta Triux) and an MRI (Siemens Prisma 3T) and is embedded in an excellent interdisciplinary scientific environment with a strong research focus on neurosensory, neurocognitive, and medical research. The successful candidate is expected to actively contribute to the implementation of neuroscience data acquisition, storage, and reproducible analysis pipelines building on the BIDS standard at the University of Oldenburg, to contribute to community efforts, and dissemination. Therefore, candidates are expected to have an academic university degree (Master or equivalent) in the field of informatics, engineering, neuroscience or psychology and have shown their ability to perform excellent scientific work, demonstrated by the outstanding quality of their doctorate/PhD research and an excellent publication record. Prior experience with the BIDS standard as well as its programming, experience with neuroimaging techniques and data analysis (especially fMR or MEG/EEG) and fluency in English is required. Experience with open science tools and databases, other neurophysiological modalities, as well as knowledge of German are desirable. The University of Oldenburg is dedicated to increase the percentage of female employees in the field of science. Therefore, female candidates are strongly encouraged to apply. In accordance to § 21 Section 3 NHG, female candidates with equal qualifications will be preferentially considered. Applicants with disabilities will be given preference in case of equal qualification. Please send your application including a cover letter, CV, list of potential referees, links to recent publications and copies of certificates for academic grades to Prof. Jochem Rieger, Department of Psychology, University of Oldenburg, 26111 Oldenburg, Germany; (jochem.rieger(a)uni-oldenburg.de <mailto:jochem.rieger@uni-oldenburg.de>). Electronic applications (one pdf file) are preferred. For inquiries please use the same contact. The application deadline is*15th of November 2020*. -- Prof. Dr. rer. nat. Jochem Rieger Head of Applied Neurocognitive Psychology Head of Neuroimaging Unit Faculty VI Carl-von-Ossietzky University 26111 Oldenburg Germany Phone: +49(0)4417984533 Fax: +49(0)4417983865

Nov. 3, 2020

computational neuroscience postdoc at Harvard

by Sam Gershman

The Gershman lab <http://gershmanlab.webfactional.com> at Harvard University is seeking a postdoctoral fellow to work on modeling of the basal ganglia and dopamine function. The postdoc will work closely with experimentalists as part of an NIH-funded U19 grant. Candidates must have a strong background in computational neuroscience and reinforcement learning models. Experience with neural data analysis is desirable but not required. The start date for this position is on or around September 1, 2021, but this can be flexibly adjusted as needed. The position is fully funded for 3 years. We are an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law. Interested applicants should contact Sam Gershman (gershman(a)fas.harvard.edu) along with a CV and list of references.

Nov. 3, 2020