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

The Annual BiasWatchNeuro Award for Equity and Inclusivity

by Bias WatchNeuro

We wanted to let you know of this new award, for a department/institute/program that is making special (and effective) efforts to ensure inclusivity and equity for trainees from minoritized and historically marginalized group. We hope you will circulate the below call for nomination among trainees in your department. Letters of nomination are due by end of August, for a September award date (in time for graduate recruiting season). Even if your department does not win this year, letters of nomination for the winning departments will be made public, so other departments can learn and copy their best practices. We are looking forward to a day where all neuroscientists feel welcome and supported in any university. The call for nominations is below, and also at https://biaswatchneuro.com/bwn-award/. > Call for nominations The Annual BiasWatchNeuro Award for Equity and Inclusivity > > Diverse voices and ideas deserve to be heard equitably in science. Since > 2015, BiasWatchNeuro has worked to increase the representation of women in > neuroscience and related fields, emphasizing in particular the > representation of women as invited speakers at conferences. However, women > are not the only group that is confronted with implicit biases and systemic > obstacles in science. Minoritized groups are severely underrepresented at > every level of the academic career path — from undergraduate education to > faculty. Attempts to diversify departments have increased, but the reality > is that many universities and institutions still embody and perpetuate both > the historical influence of being established by men of privilege, and the > persisting effects of systemic racism in our society. Even as more diverse > student bodies are recruited, the culture in many departments and > institutions is not welcoming to and supportive of those that belong to > minoritized groups. Intersectionality adds another layer of disadvantage, > with minoritized women being especially underrepresented and unsupported. > > It is time to change this reality and build a new one, in our departments > and institutions. Black scientists matter. Latinx scientists matter. > LGBTQAI+ scientists matter. First generation scientists matter. Low income > scientists matter. Intersectionality matters. > > BiasWatchNeuro is excited to announce a new Annual Award for Equity and > Inclusivity, awarded to a neuroscience or neuroscience-related department, > institute or program that demonstrates the exceptional creation of a > culture where individuals underrepresented and/or marginalized in STEM feel > integral to the community and thrive. > > We recognize that no department/institute/program is perfect. However, > some are doing much better than others, and should be recognized for this. > Nomination letters for winners and runner ups will be made public (without > the list of signatories, which will remain confidential), to showcase > successful methods for creating an inclusive and equitable culture, and to > provide prospective trainees at all levels with information that can inform > their decisions of where to apply to. We hope that this will help us all > improve our practices and move toward a day in which all neuroscientists > feel seen, respected, and supported. > > Nominations for the 2020 award will be accepted through *August 31, 2020*. Awards > will be announced in September. > > Letter of nomination signed by one or more trainees (current and/or > alumni; including post-bacc/RAs; faculty cannot nominate their current > program) should be sent to biaswatchneuro(a)gmail.com. Letters should > describe in detail specific actions and elements that promote inclusivity > and equity, and their impact on underrepresented/marginalized groups. More > than one letter and/or letters with multiple signatories will be viewed > favorably. > Sincerely, The BiasWatchNeuro team ----------------------------------------------------- Please feel free to send conferences and meetings our way by filling out this <https://docs.google.com/forms/d/e/1FAIpQLSe5ydak4RqHyrVU2BGc17T_SXsFiYB9j_Y…> form. For more information: www.biaswatchneuro.com

July 20, 2020

Invitation for papers submission to In Silico Pharmacology

by boris gutkin

On behalf of the In Silico Pharmacology (Springer) editorial board, we would like to invite papers at the interface between computational neuroscience, artificial intelligence, machine learning and neuropharmacology. In Silico Pharmacology provides a forum for peer-reviewed research articles at the cross-roads of computation, neuroscience, pharmacology and toxicology. It is anticipated that all computational and experimental approaches are represented within In Silico Pharmacology. The journal primarily publishes interdisciplinary papers that address computational approaches in multi-scale analysis of bioactive substances from the cellular up to behavioral level as well as drug-design. The journal especially encourages deterministic and stochastic modeling of biological (e.g., biochemical, biophysical and immunological) processes leading to therapeutic advancements, as well as mathematical methods characterizing the pharmacology of substances within the living organism. Papers investigating substance- or material-induced morphological and genetic alterations are also welcome. More information can be found at the journal website: https://www.springer.com/journal/40203/

July 20, 2020

PhD Position in Computational Neuroscience at the University of Edinburgh

by CHADWICK Angus

Applications are invited for a fully-funded 3 year PhD studentship in Computational Neuroscience with Dr. Angus Chadwick at the Institute for Adaptive and Neural Computation in the School of Informatics, University of Edinburgh. Applicants should hold, or be close to completion of, an undergraduate or masters degree in physics, mathematics, computer science, engineering, or a related subject, and be interested in applying their analytical skills to tackle problems in neuroscience. Highly motivated students with other backgrounds may also apply. Research in our group focuses on the neural circuit computations underlying perceptual and cognitive function, with a focus on vision and spatial navigation. We use a combination of approaches, including 1) analysis and simulation of biological neural networks, 2) development of novel data analytic methods for large-scale neural recordings, and 3) normative models of neural circuit function informed by machine learning and artificial intelligence. Typical techniques used include dynamical systems theory, statistical physics, signal processing and machine learning. We collaborate closely with experimental neuroscience laboratories both in Edinburgh and further afield. A number of projects are available, and there is flexibility to develop a project to suit the interests and skills of the candidate. Edinburgh is a vibrant and international city with a large student population, and has been voted as “best place to live in Britain”. The School of Informatics hosts an internationally-leading research environment in Computational Neuroscience, Machine Learning and Robotics, with close links to the Centre for Discovery Brain Sciences and the School of Philosophy, Psychology and Language Sciences. Applicants should email Dr. Angus Chadwick directly at angus.chadwick(a)ed.ac.uk with their CV and a brief statement of interest, or for informal enquiries and discussion. Applications will be considered until the position is filled. The start date for the position is flexible (with earliest possible start September 2020). The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

July 20, 2020

Release of CARLsim5 - Latest version of our GPU-accelerated Spiking Neural Network Simulator

by Jeffrey Krichmar

Dear Colleagues, We are pleased to announce the release of CARLsim5. CARLsim is an efficient, easy-to-use, GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides an intuitive programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level. The new release has a python frontend that is compatible with PyNN. Software and user documentation can be found at: https://github.com/UCI-CARL/CARLsim5 New and improved features in CARLsim5 include: · PyNN compatibility · Neuron monitor for observing the voltage and current traces of individual neurons · Improved installation for the Evolutionary Computations in Java (ECJ) interface (coming soon) · Docker images for Windows users and computer cluster users · Saving and loading simulations For those interested in the pyCARL interface, our IJCNN paper will be presented at the Plenary Poster Session I-P7: Spiking Neural Networks, Tuesday, July 21, 2:30PM-4:30PM GMT+1), IJCNN Poster Room 1: P1317 PyCARL: A PyNN Interface for Hardware-Software Co-Simulation of Spiking Neural Network [#20903] Sincerely, The CARLsim team Jeff Krichmar Department of Cognitive Sciences 2328 Social & Behavioral Sciences Gateway University of California, Irvine Irvine, CA 92697-5100 jkrichma(a)uci.edu http://www.socsci.uci.edu/~jkrichma

July 19, 2020

The Journal of Mathematical Neuroscience - recent articles

by Stephen Coombes

The Journal of Mathematical Neuroscience publishes research articles on the mathematical modelling and analysis of all areas of neuroscience. The current list of journal articles is available at http://www.mathematical-neuroscience.com/ : Methods to assess binocular rivalry with periodic stimuli Authors: Farzaneh Darki and James Rankin https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Understanding the dynamics of biological and neural oscillator networks through exact mean-field reductions: a review Authors: Christian Bick, Marc Goodfellow, Carlo R. Laing and Erik A. Martens https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Spatially extended balanced networks without translationally invariant connectivity Authors: Christopher Ebsch and Robert Rosenbaum https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Geometry of color perception. Part 1: structures and metrics of a homogeneous color space Authors: Edoardo Provenzi https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… Mesoscopic population equations for spiking neural networks with synaptic short-term plasticity Authors: Valentin Schmutz, Wulfram Gerstner and Tilo Schwalger https://mathematical-neuroscience.springeropen.com/articles/10.1186/s13408-… All articles are Open Access. The Impact Factor of the journal is 2.091 ------------------------------------------------------- Stephen Coombes Professor of Applied Mathematics School of Mathematical Sciences Nottingham, UK Tel: 0115 846 7836 http://www.maths.nott.ac.uk/~sc/ ------------------------------------------------------- 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.

July 17, 2020

3 PhD/MSc Positions at the University of Calgary

by Wilten Nicola

The Nicola Computational Neuroscience lab at the University of Calgary in the Hotchkiss Brain Institute is looking for three talented researchers at the PhD/Masters level. *PhD/MSc Position 1: Analysis and Modelling of Trained Recurrent and Spiking Neural Networks * The Nicola Lab is looking for a talented Master's or PhD candidate with a strong background in pure or applied mathematics, or physics. The project will involve analyzing the structure and operation of trained spiking and recurrent neural networks to determine how these trained networks perform dynamics, solve tasks, and emulate behaviours. The ideal candidate will have a background in dynamical systems theory, functional analysis, and some statistical analysis, and have a BSc in pure or applied mathematics. Some knowledge of numerical methods and neuroscience is beneficial, but not required. *PhD/MSc Position 2: Modelling Spatiotemporal dynamics in whole-brain imaging* We are looking for a talented Master's or PhD candidate with a background in computational neuroscience, mathematics, or physics. The project will involve analyzing the emergent spatiotemporal dynamics of whole-brain Calcium imaging data obtained in the McGirr Lab for mice undergoing experimentally induced stress paradigms. The ideal candidate will have a background in dynamical systems theory, statistical analysis, and a particular focus on spatial models (Partial Differential Equations), or Markov Processes. The ideal candidate will have a background in scientific programming and numerical methods for the simulation and analysis of these models. *PhD/MSc Position 3: Investigating Synchrony in Spiking Neural Networks * The Nicola Lab is looking for a talented Master's or PhD candidate with a strong background in Applied or Pure mathematics with an emphasis on dynamical systems theory. The project will involve analyzing the synchronizability of non-smooth, integrate-and-fire type spiking neural networks under a variety of conditions. The ideal candidate will have a background in dynamical systems theory, functional analysis, and some statistical analysis, and have a BSc in pure or applied mathematics. The ideal candidate will have a background in scientific programming and numerical methods for conducting simulations. Interested candidates should clarify which position they are applying for in an email to wilten.nicola(a)ucalgary.ca and attach to this email their CV, undergraduate/master's degree transcripts, a letter of research interests, and the contact information for 2 referees. The start-dates are flexible. The University of Calgary is a global intellectual hub located in Canada’s most enterprising city. In our spirited, high-quality learning environment, students thrive in programs made rich by research, hands-on experiences and entrepreneurial thinking. Our strategy drives us to be recognized as one of Canada’s top five research universities, engaging the communities we both serve and lead. This strategy is called Eyes High, inspired by the university's Gaelic motto, which translates as 'I will lift up my eyes.' For more information, visit ucalgary.ca/eyeshigh.

July 17, 2020

Scientific software developer position at the SimLab Neuroscience, Juelich, Germany

by Charl Linssen

(with apologies for any cross-posting) Dear colleagues, We have a Scientific software developer position available in the SimLab Neuroscience at the Jülich Supercomputing Centre, Jülich Research Centre, Germany. We are looking for candidates with a proven track record in developing scientific software who are interested in further developing NESTML, a modelling language and corresponding toolchain for the convenient specification of neuron and synapse models and the automatic generation of efficient C++ code from this specification modelling language. For a full description and details of how to apply, please see the announcement on our website: *Scientific Software Developer in Computational Neuroscience* https://www.fz-juelich.de/SharedDocs/Stellenangebote/_common/dna/2020-230-E… The application deadline for the position is August 5th. Thank you for your consideration! With kind regards, Charl Linssen _____________________________________ Charl Linssen Ir. MSc SimLab Neuroscience / IAS-6 Jülich Supercomputer Centre (JSC) Institute for Advanced Simulation Forschungszentrum Jülich GmbH c.linssen(a)fz-juelich.de +49 (0)2461 61-5269 _____________________________________

July 16, 2020

IMRF2020 postponed to June 07-10 2021 in Ulm, Germany

by Marc Ernst

Dear participants of the IMRF, Although, the COVID-19 situation is getting better in some places around the world, it is still getting worse in a lot of other places, and travelling to and from Germany is still far away from normal. Additionally, distancing restrictions apply and will likely apply for quite some more time (maybe until a vaccination has been found), which would not allow us to host as many people as anticipated at the venue we reserved in October 2020. As many other conferences, we also considered moving to an online format for the IMRF meeting (https://cops.ifp.uni-ulm.de/imrf2020/ <https://cops.ifp.uni-ulm.de/imrf2020/>). However, we feel the community would not benefit as much as having a meeting in person. Therefore, we decided to postpone the IMRF meeting once again (and hopefully for the last time) to June 07-10, 2021. Abstract submission and registration will stay open. All abstracts already submitted will further be considered. However, as there may be new data or insights gathered even during the COVID-19 pandemic, you can of course log on and adapt your abstracts until the new deadline for abstract submission. Same applies for the symposia already accepted. However, as the symposia have already gone through a review process, we would check these changes again and in case of substantial revisions we would probably re-review them again. We will announce the new deadlines for submission and registration in due time. The abstract submission and registration page can be found here: https://cops.ifp.uni-ulm.de/imrf2020/index.php/imrf-2020/registration-submi… <https://cops.ifp.uni-ulm.de/imrf2020/index.php/imrf-2020/registration-submi…> Also for those who already registered, your registrations will stay valid. Others can register at any time. The new registration deadlines will also be announced soon. Sorry for the inconvenience this second postponement may cause and thanks for your understanding. Be safe and stay healthy!!!! Best, Mac Ernst on behalf of the IMRF Organizers.

July 15, 2020

Professorship position in explainable/interpretable Machine Learning

by Jörg Lücke

Dear list, Let me draw your attention to a currently advertised position on explainable / interpretable learning algorithms. The position is in the Health Sciences but researchers with a data analysis background interested in developing in the direction of health data analysis are of interest. Also candidates with a computational neuroscience background or a robotics background are of interest. So the spectrum of potential candidate profiles is relatively broad. Please see the following link for the official advertisement. https://uol.de/stellen/?stelle=67364 The position is a German W2 Professorship position (similar Associate Professor). Thanks and best wishes, Jörg Lücke -- Jörg Lücke (PhD) Professor and Head of the Machine Learning Lab Department of Medical Physics and Acoustics School of Medicine and Health Sciences University of Oldenburg 26111 Oldenburg Germany www.uol.de/ml

July 15, 2020

CNS*2020 Workshop on "Multi-disciplinary approaches to quantify and model calcium signaling in nervous systems and beyond", July 21-22, 2020 (8.30 am-5 pm BST / GMT+1)

by Maurizio De Pittà

Dear colleagues, Please share it with your contacts. I am delighted to be able to share with you the finalized program of the forthcoming Workshop on "Multi-disciplinary approaches to quantify and model calcium signaling in nervous systems and beyond," July 21-22, 2020 (8.30 am-5 pm BST / GMT+1) as part of the CNS*2020 Virtual Conference. Workshop website: https://sites.google.com/view/cns2020-calcium-workshop/home We are joining together some of the prominent scientists in the field, touching a whole range of topics and approaches, ranging from techniques and machine learning tools to acquire calcium signals in living systems, to modeling in neurons, synapses, glial and other systems of the body. Confirmed speakers (in alphabetical order): Amit Agarwal, Heidelberg University, Germany Johnatan Aljadeff, University of California at San Diego, USA Alexey Brazhe, Lomonosov Moscow State University, Russia Pengxing Cao, School of Mathematics and Statistics, University of Melbourne, Australia Evan Cresswell-Clay, National Institute of Health, USA & The Basque Center for Applied Mathematics, Spain Silvina Ponce Dawson, Department of Physics, FCEN-UBA & IFIBA, CONICET-UBA, University of Buenos Aires, Argentina Martin Falcke, Max Delbrück Center for Molecular Medicine Berlin, Germany Johannes Friedrich, Simons Foundation, USA Andrea Giovannucci, UNC-Chapel Hill/North Carolina State University, USA Michael Graupner, Université de Paris, CNRS, SPPIN, France Shawn Means, School of Natural and Computer Sciences, Massey University, New Zealand Vijai Rajagopal, University of Melbourne, AUS Leonid Savtchenko & Dimitri Rusakov, Queen Square Institute of Neurology, University College London, UK Simon Schultz, Centre for Neurotechnology and Department of Bioengineering, Imperial College London, UK Alexey Semyanov, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia Ivo Siekmann, Department of Applied Mathematics, Liverpool John Moores University, UK Alexander Skupin, University of Luxembourg, Luxembourg James Sneyd, The University of Auckland, New Zealand Ghanim Ullah, University of South Florida, USA Agne Tilūnaitė, School of Mathematics and Statistics, University of Melbourne, Australia Ruediger Thul, The University of Nottingham, UK Attendance to the online Workshop is FREE but requires registration to the CNS*2020 meeting (this year free of charge). More Info: https://docs.google.com/document/d/1N45m5I4lZ4wUX4kOkxgPqEK4yeIdADuKgdqPuBF… Schedule of the Workshop's talks, along with Crowdcast links for individual sessions may be found on the Sched page of CNS*2020: https://cns2020online.sched.com/overview/type/Workshop/W02%3A+Calcium+signa… CALCIUM WORKSHOP webpage: https://sites.google.com/view/cns2020-calcium-workshop/home Thank you for your consideration. The workshop organizers: Pengxing Cao, University of Melbourne, Australia Maurizio De Pitta, Basque Center for Applied Mathematics, Spain Ivo Siekmann, Liverpool John Moores University, UK ----- Maurizio De Pitta' Research Fellow MCEN -- Group of Mathematical, Computational and Experimental Neuroscience BCAM -- Basque Center of Applied Mathematics https://sites.google.com/site/mauriziodepitta/home

July 14, 2020