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FACM-22 Conference 'New Perspectives in Math Biology' May 20-21 (2022) NJIT, Newark NJ
by Victor Matveev 01 Apr '22

01 Apr '22

On May 20 and 21, 2022, the 17th Annual Conference on Frontiers in Applied and Computational Mathematics (FACM '22) will be held at the New Jersey Institute of Technology (NJIT) in Newark, New Jersey. The theme of FACM '22 Conference is "New Perspectives in Mathematical Biology." https://sites.google.com/njit.edu/facm2022/home Confirmed plenary speakers are: Carina Curto (Pennsylvania State University) Anita Layton (University of Waterloo) Grzegorz Rempala (Ohio State University) Corina Tarnita (Princeton University) FACM '22 will feature 4 minisymposia that cover a wide range of topics in math biology: (1) *learning paradigms in real and artificial neuronal networks,* (2) collective behavior in biological populations, (3) stochastic modeling at different scales, and (4) biofluids: machine learning and data-driven approaches. A poster session will run concurrently over the 2 days of the meeting. Pending NSF support, funds to cover all or part of the travel costs and local accommodation costs may be available for students, postdocs, and junior faculty. Applications by members of underrepresented groups, minorities and women are particularly encouraged. A combined poster abstract submission, travel award application and registration form (due April 15, 2022) is available at the conference homepage: https://sites.google.com/njit.edu/facm2022/home There is no registration fee for this conference. NJIT campus is located in close proximity to two train stations, the Newark Liberty International airport, and is accessible by public transportation from New York City: https://www.njit.edu/about/maps-directions FACM'22 Organizing Committee: Amitabha Bose (co-Chair), Casey Diekman, Simon Garnier, Enkeleida Lushi, James MacLaurin, Victor Matveev (co-Chair), Peter Thomas, Yuan-Nan Young -- ----------------------------------------------- Victor Matveev, Professor Applied Math, Biophysics, Neuroscience Department of Mathematical Sciences Graduate Faculty, Dept of Biological Sciences New Jersey Institute of Technology Newark, NJ 07102-1982 matveev(a)njit.edu

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INCF/OCNS Software WG session on NetPyNE (4th April: 1600 UTC)
by Ankur Sinha 01 Apr '22

01 Apr '22

Dear all, Apologies for the cross post. Please join us for the next INCF/OCNS Software working group "dev session" where Joe Graham will speak to us about NetPyNE: https://ocns.github.io/SoftwareWG/2022/04/04/dev-session-joe-graham-netpyne… - Date: April 4, 2022, 1600 UTC (Click here[1] to see your local time). - Location (Zoom): (login to Zoom required): https://ucl.zoom.us/j/99620419452?pwd=SkZlQnJmWWZVczNURkp2azVOZkhzUT09 Abstract: NetPyNE is an open-source Python package to facilitate the development, parallel simulation, analysis, and optimization of biological neuronal networks using the NEURON simulator. The NetPyNE GUI is available from a variety of resources: Neuroscience Gateway Portal (NSG); Open Source Brain (OSB) ; Human Brain Project (HBP) EBRAINS; and the NIH SPARC initiative. The NetPyNE source code is available on GitHub. More information is available on the NetPyNE website. During this dev session, I will give an overview of NetPyNE, go through an interactive demo using the NetPyNE GUI, describe my personal development workflow using virtual environments, and then go through two big dev projects I worked on: (1) documenting code inline and online using docstrings, Sphinx, Napoleon, and autodocsumm, and (2) separating and standardizing analysis and plotting. --------- 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. If you develop software for neuroscience, we would love to hear about your development pipeline. Please get in touch with the Software WG on our GitHub repository[3]. 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://www.timeanddate.com/worldclock/fixedtime.html?msg=Dev+session%3A+Jo… [2] https://github.com/OCNS/SoftwareWG/issues -- 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

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Postdoctoral position in computational neuroscience
by Maxim Bazhenov 31 Mar '22

31 Mar '22

Applications are invited for NIH funded post-doctoral research position in the laboratory of Dr. Maxim Bazhenov at the University of California, San Diego to study role of sleep in memory and learning using sophisticated computer models of brain dynamics. This project involves close collaboration with experimental laboratories. The ultimate goal of the work is to understand how sleep rhythms contribute to consolidation of memory for recent learning and how sensory or electrical stimulation during sleep can enhance memory consolidation (see, e.g., 10.7554/eLife.51005; 10.1093/cercor/bhaa228; 10.1523/JNEUROSCI.1427-19.2019). Our lab research interests also include other topics in neuroscience (e.g., olfaction, epilepsy) and artificial intelligence (e.g., lifelong learning, generalization, adversarial robustness) and lab members are encouraged to participate in multiple projects. The successful candidate will be responsible for the design of the anatomically realistic brain network models based on experimental data. These models will be used to understand network dynamics that are involved in the processes of memory consolidation during sleep, as well as guide data analysis and produce novel experimental predictions. Qualified applicants are expected to have background and experience in neuroscience, computational neuroscience, physics/engineering and/or mathematics. Programming experience with C/C++ is required. Knowledge of PYTHON, PyTorch or MATLAB is a plus. The University of California offers excellent benefits. Salary is based on research experience. Applicants should send a brief statement of research interests, a CV and the names of three references to Maxim Bazhenov at mbazhenov(a)ucsd.edu -- Maxim Bazhenov, Ph.D. Professor, Department of Medicine, Neurosciences Graduate Program, UCSD, School of Medicine http://www.bazhlab.ucsd.edu/

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Google Summer of Code: model and experimental data sharing on Open Source Brain
by Padraig Gleeson 31 Mar '22

31 Mar '22

--Apologies for cross-posting-- Google Summer of Code <https://summerofcode.withgoogle.com/> is a global, online program focused on bringing new contributors into open source software development. Generous stipends are provided for successful applicants to work on these projects for a number of months over the summer. The INCF <http://incf.org/> has been a GSoC mentoring organisation for the past number of years, and has helped link up students with mentors to advance various projects in the wider neuroinformatics and computational neuroscience areas. The Open Source Brain initiative <http://www.opensourcebrain.org> is encouraging students to apply to be part of this. The successful candidate(s) for our 2 proposals will take published computational models and experimental datasets and convert them into open, standardised formats (e.g. NeuroML and NWB) and share them on the OSB platform as a resource for the wider community. The two projects are: *Open source, cross simulator, large scale cortical models in NeuroML and PyNN* <https://neurostars.org/t/gsoc-2022-project-idea-9-1-open-source-cross-simul…> These can be models where code is available in simulator specific formats on ModelDB, or classic models from the literature which would benefit from curating/updating/documenting. Making models available in these formats will allow them to be used & tested across multiple simulators, make the physiological properties of the models more accessible and facilitate reuse of model components. *Conversion of public neurophysiology datasets to Neurodata Without Borders (NWB) format* <https://neurostars.org/t/gsoc-2022-project-idea-9-2-conversion-of-public-ne…> This project will involve converting a number of publicly available datasets to NWB format, adding structured metadata to ensure maximal readability and reusability of the data. The converted datasets will be made available through the new NWB Explorer on the Open Source Brain repository (http://nwbexplorer.opensourcebrain.org) which allows visualisation of the data as well as interactive analysis through an inbuilt Jupyter notebook. *This opportunity is particularly relevant for Masters & PhD students currently working in model development/data analysis in neuroscience. Many students **are already reusing/converting/updating existing models and data as part of their work and this is a great opportunity to get paid extra to do this! *** Closing date for student applications: *19 April 2022* Period of working on projects: *13 June - ***12 *September 2022* Please get in contact if you have any questions. -- ----------------------------------------------------- Padraig Gleeson Room 321, Anatomy Building Department of Neuroscience, Physiology& Pharmacology University College London Gower Street London WC1E 6BT United Kingdom +44 207 679 3214 p.gleeson(a)ucl.ac.uk -----------------------------------------------------

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Postdoc in Computer Vision / Machine Learning / Applied Mathematics
by Tony Lindeberg 31 Mar '22

31 Mar '22

Postdoc in Computer Vision / Machine Learning / Applied Mathematics Job description The Division of Computational Science and Technology at KTH Royal Institute of Technology in Stockholm, Sweden is seeking a Postdoc in Computer Vision / Machine Learning / Applied Mathematics to handle scale-dependent image information in deep networks. In our research, we develop deep networks for processing image data that handle scaling transformations and other image transformations in a theoretically well-founded manner. Our research in this area comprises both theoretical modelling of the influence of image transformations on different architectures for deep networks and the experimental evaluation of such networks on benchmark datasets to explore their properties. The work also comprises the creation of new benchmark datasets, to enable characterization of properties of deep networks that are not covered by existing datasets. For examples of our previous work in this area, see https://www.kth.se/profile/tony/page/deep-networks Within the scope of this postdoc position, you are expected to work on and contribute to the research frontier regarding scale-covariant or scale-equivariant deep networks and/or deep networks parameterized in terms of Gaussian derivatives, on specific research topics that we choose together. The selected candidate will work closely together with the project leader Tony Lindeberg. Qualifications requirements * A doctoral degree or an equivalent foreign degree, obtained within the last three years prior to the application deadline * We are seeking a candidate with a PhD in Computer Vision, Machine Learning, Applied Mathematics or a related discipline dealing with automated analysis of image information. * Previous experience with experimental evaluations using deep learning architectures applied to image data is necessary, preferably PyTorch. * A theoretical background in continuous mathematics for modelling convolutions and the influence of image transformations on image data is also necessary. Preferred qualifications As a person you have excellent scientific and collaborative skills, in combination with independence, with very good ability to get into new scientific theories and conduct implementations and experimental evaluations in close collaboration with the research environment you are working in. The preferred candidates should have demonstrated expertise (through publications) in any one of the following: * Deep networks that handle image information for computer vision tasks, including experimental evaluation using modern architectures for deep networks. * Continuous models for deep networks applied to image information. * Theoretical modelling of scaling transformations or other image transformations applied to automated processing of image information. For further information and information about to how to apply, see https://www.kth.se/en/om/work-at-kth/lediga-jobb/what:job/jobID:490734/ Application deadline: May 2, 2022 The position is offered for a period of two years. [cid:FD2B374F-C472-4895-ADA7-B3CD5419FD22@csc.kth.se] Tony Lindeberg Professor of Computer Science — Computational Vision KTH Royal Institute of Technology Computational Brain Science Lab Division of Computational Science and Technology, CST SE-100 44 Stockholm, Sweden Phone: +46 8 790 6205 https://www.kth.se/profile/tony/

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Cerebellar computation postdoc
by Nicolas Brunel 30 Mar '22

30 Mar '22

A postdoc position is available to build and analyze network models of cerebellar cortex that incorporate the diversity of cell types and synaptic connections observed in this structure. The goal of this research is to better understand the functions of these diverse cell types and connections. Approaches from statistical physics, nonlinear dynamics and machine learning will be used, and models will be constrained by new electrophysiological, transcriptomic and connectomic data. The postdoc will be jointly supervised by Wade Regehr (Department of Neurobiology at Harvard Medical School) and Nicolas Brunel (Duke University). The position will be based in Wade Regehr's lab, but with frequent visits to the Brunel lab at Duke. Applicants should have a strong background in computational/theoretical neuroscience, machine learning, theoretical physics, and/or applied mathematics. We are committed to building a diverse intellectual community, and particularly encourage women and members of underrepresented groups to apply to this position. For more information on the labs: Regehr Lab: https://urldefense.com/v3/__https://regehrmedharvard.wordpress.com/__;!!OTo… Brunel Lab: https://www.neuro.duke.edu/research/faculty-labs/brunel-lab Please email a cover letter explaining background and interest in the position, a curriculum vitae, and names & email addresses of two references to: Kim McDaniels Kimberly_Mcdaniels(a)hms.harvard.edu<mailto:Kimberly_Mcdaniels@hms.harvard.edu> Please have the subject of the email: “Computational Postdoc Applicant:” Your Name

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IMRF abstract submission deadline extended to April 07
by Marc Ernst 30 Mar '22

30 Mar '22

Dear friends of IMRF, upon multiple request, we decided to extend the abstract submission deadline for the International Multisensory Research Forum 2022 (IMRF2022) by some days to April 07th. You can submit new abstracts for talks and posters until that date (here <https://www.conftool.net/imrf2020>). In case you submitted an abstract already previously for 2020 or 2021, please make sure to verify that your abstract and information is still up-to-date. To do so, you can log into the system (here <https://www.conftool.net/imrf2020>) and update your abstract information at any time until the deadline. In case you will not be able to make it to IMRF this year, which I would deeply regret, but you submitted an abstract earlier in the past two years, please make sure to withdraw your abstract (here <https://www.conftool.net/imrf2020>). In case you submitted an already accepted symposium in 2020, these symposia will keep their accepted status. But please as organiser of the symposium verify that all presenters of the symposia are still on board (here <https://www.conftool.net/imrf2020>). In cases where this is necessary please update the symposium information - abstracts of the symposia can be updated by the organiser of the symposium. In case you have a drop out of one or two speakers it is best to exchange them by new speakers. As for registration, I would recommend to register early (here <https://www.conftool.net/imrf2020>). At the moment it seems like the spatial restrictions may be loosened. But with this virus you never know. Also, please start looking for a hotel room early. There is the Danube Festival the same week of IMRF - a nice festival along the Danube river. We reserved some rooms but only until a month prior to the meeting. When booking, please refer to “IMRF” to get our conference rates. Looking forward to finally seeing you in Ulm in summer 2022. Best, Marc --------------------------------------------------------- Prof. Dr. Marc Ernst Applied Cognitive Psychology Faculty for Computer Science, Engineering & Psychology Ulm University Albert-Einstein-Allee 43 89081 Ulm room nr.: 43.3.103 mail: marc.ernst(a)uni-ulm.de <mailto:marc.ernst@uni-ulm.de> phone int.: +49-(0)731-50 320 50 phone ext.: +49-(0)731-50 356 27 sekr: +49-(0)731-50 320 51 mobile: +49-(0)152-22 543 156

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Workshop: The interplay of complex and coherent dynamics in brain function. May 18-20, Cergy
by boris gutkin 29 Mar '22

29 Mar '22

Interplay of complex and coherent dynamics in brain function will take place at CY Advanced Studies at Neuville-Sur-Oise from 18th to 20th May 2022 thanks to the support of CY Cognition, CYAS, Labex MME-DII. More information can be found here: https://complexityparisseine.wordpress.com/ The workshop will take place in a hybrid form, with a group of participants (at most 50) in presence at CYAS and the rest connected via Zoom. There will be the possibility to present posters of your research activity up to a maximum of 20 posters, There are no costs, but if you are interested you should register in both cases either in presence or in remote (Zoom) by April 30th. Organisers: Alessandro Torcini (CYU), Demian Battaglia (INS marseille), Boris Gutkin (ENS, Paris) and Matteo di Volo (University of Parma, Italy)

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additional 2 postdoc positions (4 in total) at Imperial College
by Schultz, Simon R 29 Mar '22

29 Mar '22

Dear all, In addition to the previously advertised two experimental positions, we have two theoretical postdoc positions available: Four post-doc positions in the Statistical Physics of Cognition Two theoretical and two experimental postdoctoral positions each for a duration of up to 36 months starting as soon as possible after 1st April 2022. All four post-docs will form a collaborative team, will be affiliated with the Departments of Mathematics and Bioengineering at Imperial College London, and will work together with a core team consisting of Simon R Schultz, Henrik Jeldtoft Jensen, Fernando Rosas, Mauricio Barahona, Lucilla de Arcangelis, Ann Go and Amanda Foust. As for the two theoreticians we are looking for people familiar with statistical mechanics of complex systems, including SOC, network theory and information theory. The theory positions can be found here: https://www.imperial.ac.uk/jobs/description/NAT01116/research-associate-mat… The details for the experimental positions are here: https://www.imperial.ac.uk/jobs/description/ENG02064/postdoctoral-research-… To discuss the theoretical positions, please contact Henrik Jensen (h.jensen(a)imperial.ac.uk<mailto:h.jensen@imperial.ac.uk>) To discuss the experimental positions, please contact Simon Schultz (s.schultz(a)imperial.ac.uk<mailto:s.schultz@imperial.ac.uk>) Best wishes Simon -- Prof Simon Schultz Dept of Bioengineering, Imperial College London http://www.schultzlab.org Director, Imperial College Centre for Neurotechnology http://www.imperial.ac.uk/neurotechnology For Centre admin, email: Dr Kate Hobson, k.hobson(a)imperial.ac.uk

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Atsushi IRIKI speaking on March 31 in Developing Minds global online lecture series
by Jochen Triesch 28 Mar '22

28 Mar '22

Dear colleagues, On March 31, the Developing Minds global online lecture series will feature Atsushi IRIKI, RIKEN Japan: "Self-in-the-world map evolved in the primate brain as a basis of civilized Homo sapiens“ The live event will take place via zoom at: 22:00 JST (Japan Standard Time) 15:00 CET (Central European Time) 13:00 UTC (Universal Coordinated Time) 9:00 EST (Eastern Standard Time) To participate please register here: https://sites.google.com/view/developing-minds-series/home Abstract After a specific point in history, hominin evolution accelerated to a level that could not be accounted for by natural selection alone, but an alternative mechanism has been proposed based on mutual interaction among neural, cognitive, and ecological niches in a positive feedback loop (triadic niche construction; TNC). Nevertheless, the trigger events for the cognitive revolution of Homo sapiens as well as the reasons for this event being limited to a single species remain unknown. Using a multidisciplinary approach involving psychology, neurobiology, and phenomenology, I will propose a shift in the mechanisms underlying TNC, from TNC- 1 in primates/hominids to TNC-2 in Homo sapiens, to answer these questions. As the primates and hominin brain expanded during TNC-1, latent cognitive capabilities were incubated within its neural framework to be expressed with a simple rewiring among brain areas in TNC-2, a quick and inexpensive process but one that requires a unique set of preconditions to commence. This process was bootstrapped by the advanced function of “projection,” which enabled humans to recognize the “self” in particular time and space in the world, allowing the manipulation of this world (in both physical and symbolic dimensions) again in a positive feedback loop. Based on these, a new concept of a somatocentric holistic self will be proposed, represented as a more comprehensive body-in-the-world map in the primate brain, taking into account evolutionary aspects that characterize the human cognition and its implication in the emergence of self-consciousness. Paper: Iriki A, Suzuki H, Tanaka S, Bretas R, Yamazaki Y. (2021). The sapient paradox and the great journey: Insights from cognitive psychology, neurobiology and phenomenology. Psychologia, https://doi.org/10.2117/psysoc.2021-B017. Bio Atsushi IRIKI received his Ph.D. in Neuroscience from Tokyo Medical and Dental University in 1986. He held research associate positions at the Tokyo Medical and Dental University and then at The Rockefeller University (USA). He joined the faculty of Toho University Medical School as an assistant professor and then as an associate professor in Physiology (1991-1999). In 1999, he returned to Tokyo Medical and Dental University as a full professor and chairman of Cognitive Neurobiology. In 2004, Atsushi IRIKI was appointed a head of Laboratory for Symbolic Cognitive Development at RIKEN Institute (first at its Brain Science Institute and then 2018 onward at Center for Biosystems Dynamics Research). He is currently a visiting professor of University College London (UK) and Nanyang Technological University (NTU, Singapore), an adjunct professor of Keio University, a research professor of Kyoto University, a senior fellow of the Canadian Institute for Advanced Research (Canada), founding co-director of RIKEN-NTU Research Centres (Singapore & Japan). Web: https://www.riken.jp/en/research/labs/bdr/symbol_cogn_dev/index.html Best regards, Jochen Triesch -- Prof. Dr. Jochen Triesch Johanna Quandt Chair for Theoretical Life Sciences Frankfurt Institute for Advanced Studies and Goethe University Frankfurt http://fias.uni-frankfurt.de/~triesch/ Tel: +49 (0)69 798-47531 Fax: +49 (0)69 798-47611

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