- Comp-neuro - lists.cnsorg.org

NeuroFedora: ready to use/install ISO for computational neuroscience available
by Ankur Sinha Nov. 8, 2019

Nov. 8, 2019

Hello, The NeuroFedora community is pleased to announce its first deliverable: a ready to use/install Fedora based ISO image that includes a plethora of computational neuroscience software[1]. It currently includes: auryn, bionetgen, calcium-calculator, COPASI, qalculate, getdp, genesis-simulator, gnuplot, moose, nest, neuron, neurord, octave, paraview, python3, brian2, ipython, nest, neuron, libNeuroML, neo, nineml, PyLEMS, smoldyn and the Python science stack: matplotlib, jupyter notebook, numpy, pandas, pillow, scikit-image, scikit-learn, scipy, statsmodels, and sympy. The ISO image is a "live" image and can be used without installing the operating system. It can be obtained here[1] with more information on NeuroFedora available here[2,3]. NeuroFedora is a Free/Open Source Software community based volunteer initiative. We are always looking for more volunteers to help with the work[4]. It is an excellent project for students new to computational neuroscience to learn valuable technical skills while aiding the neuroscience community. Feedback is always welcome. Please get in touch using one of our communication channels[5]. [1] https://docs.fedoraproject.org/en-US/neurofedora/install-media/ [2] https://docs.fedoraproject.org/en-US/neurofedora/ [3] https://neuroblog.fedoraproject.org [4] https://docs.fedoraproject.org/en-US/neurofedora/contributing/ [5] https://docs.fedoraproject.org/en-US/neurofedora/communicating/ On behalf of the NeuroFedora community, -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in PhD candidate in computational neuroscience at UH Biocomputation | http://biocomputation.herts.ac.uk/ Free/Open source community volunteer at the Fedora project | https://fedoraproject.org/wiki/User:Ankursinha Time zone: Europe/London

1 0

PhD in computational neuroscience, University of Edinburgh
by Matthias Hennig Nov. 6, 2019

Nov. 6, 2019

We invite applications for our fully funded PhD programme in COMPUTATIONAL NEUROSCIENCE and NEUROINFORMATICS at the School of Informatics, University of Edinburgh, for a start in or around September 2020. The studentships are ideal for students who want to apply their computational and analytical skills to problems in neuroscience and related fields. The following supervisors have openings: Douglas Armstrong: Molecular neuroinformatics, network models, behavioural models, molecular drug design. Angus Chadwick (joining early 2020): Visual and spatial processing, network dynamics, neural data analysis. Matthias Hennig: Learning and homeostasis, analysis of large-scale electrophysiological recordings. Arno Onken: Probabilistic models, dimensionality reduction, information theory. Peggy Seriès: Bayesian approaches to cognition and perception, computational psychiatry. Ian Simpson: Regulatory genomics, developmental disorders. Barbara Webb: Perceptual systems for the control of behaviour, robot models of animals. The PhD project can be done in collaboration with one of the many affiliated departments and institutes. Edinburgh has been voted as 'best place to live in Britain', and has many exciting cultural and student activities. Students with a strong background in either computer science, mathematics, physics or engineering are particularly welcome to apply. Motivated students with other backgrounds will also be considered. For more information, see: http://web.inf.ed.ac.uk/anc/research/neuroscience There is no fixed deadline, but applications completed by 29 Nov 2019 will be considered in a first round, with decisions expected by late January 2020. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

Competition funded PhD position on computational sensorimotor control @ U of Birmingham and U of Warwick
by Sang-Hoon Yeo Nov. 6, 2019

Nov. 6, 2019

Title: The integration of visually-guided interception with balance Supervisors: Dr R Reynolds (Bham), Dr Sang-Hoon Yeo (Bham) and Prof James Tresilian (Warwick) Type: Competition Funded PhD Project (European/UK Students Only) Project Description Control of fast interceptive movements is the highlight of human sensorimotor behaviour, whose flexibility and adaptability far surpasses that of any existing robot. The neural control mechanism of interceptive movement remains elusive. For example, when an object that we are reaching for moves unexpectedly, the hand is ‘magnetically’ drawn towards the new object location. These trajectory adjustments occur within a remarkably short latency (<100ms), do not require conscious awareness of the change, and may rely upon sub-cortical neural circuitry[1]. We have demonstrated that this exceptionally fast visuomotor system also controls the lower limb when attempting to step onto a moving target [2]. However, when standing, such automatic adjustments may threaten balance, which is also largely controlled by sub-cortical brain circuitry. For example, reaching for a moving object (e.g. catching a ball), causes a concomitant shift of the centre of mass which disturbs the balance, but we rarely fall. The apparently contradictory requirements of reaching and balancing must therefore be somehow seamlessly integrated at a low neural level. Staying upright in the face of such self-imposed perturbations is natural for humans, but we still do not understand the underlying mechanism(s). For example, attempts to implement such control into bipedal robots often leads to catastrophic falls (see DARPA challenge https://bit.ly/1Il2QVS) This failure to coordinate interception and balance can also lead to human falls as a result of neural degeneration (e.g. ageing). We plan to investigate the integration of these two systems, balance and interception, at both a behavioural and neural level, to address the following questions: How are balance and visually-guided interception integrated, and what are the limits of this process? What neural circuitry underlies this integration? How does normal ageing affect the integration process, and what are the consequences for fall risk? We will address these questions using a combination of techniques from Biomechanics, Neurophysiology and Robotics. To study the integration of balance and interception we will use virtual reality to present visual interception targets. This will allow us to subtly manipulate the relationship between hand and target motion [3]. Limb trajectory will be recorded using motion capture and processed in real-time to manipulate visual feedback. Balance will be simultaneously assessed by measuring ground reaction forces and full-body motion capture. The limits of the integration process (i.e. when do you fall?) will first be tested in young healthy individuals. To understand the neural circuitry we will use Transcranial Magnetic Stimulation (TMS)[4], Electromyography and H-reflexes. These techniques will allow us to determine the relative contribution of cortical and sub-cortical brain areas to these behaviours. This, in turn, will also have relevance for understanding rehabilitation of balance following brain injury. Finally, we will study older adults. This will determine the extent to which the ability to combine interception and balance is compromised by the ageing process, and the relevance for fall risk. Funding Notes This project is funded by the Midlands Integrative Biosciences Partnership. MIBTP is a BBSRC funded Doctoral Training Partnership between the University of Warwick, the University of Birmingham, the University of Leicester and Aston University and Harper Adams University. Successful candidates will start in October 2020. Candidates can apply via the MIBTP website (Weblink coming here soon) but are strongly encouraged to contact Raymond Reynolds for further information prior to applying (r.f.reynolds(a)bham.ac.uk) References 1. B.L. Day, P. Brown, Evidence for subcortical involvement in the visual control of human reaching, Brain. 124 (2001) 2. R.F. Reynolds, B.L. Day, Rapid visuo-motor processes drive the leg regardless of balance constraints, Curr. Biol. 15 (2005). 3. S.H. Yeo, D.W. Franklin, D.M. Wolpert, When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing, PLoS Comput. Biol. 12 (2016). 4. W. Marinovic, C.S. Reid, A.M. Plooy, S. Riek, J.R. Tresilian, Corticospinal excitability during preparation for an anticipatory action is modulated by the variability of visual information, J. Neurophysiol. 105 (2011).

1 0

Call for PhD positions in Computational Neuroscience|Cognitive Science| Psychology|Neurophysics @ IMPRS NeuroCom
by Martin Bogdan Nov. 6, 2019

Nov. 6, 2019

***Call for applications The International Max Planck Research School on Neuroscience of Communication: Function, Structure, and Plasticity (IMPRS NeuroCom) offers several positions for excellent students holding a master's degree (or equivalent) to perform research resulting in a PhD in the field of Cognitive Neuroscience and Neurophysics. The IMPRS NeuroCom is based at the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig and Leipzig University and also involves the Max Planck Institute for Evolutionary Anthropology, Leipzig, and the Institute of Cognitive Neuroscience at the University College London, UK. ****Deadline for applications is 10 November 2019. Interviews will take place in January 2020. Starting date is flexible, but not later than autumn 2020. The IMPRS NeuroCom aims to recruit and educate motivated, independent, self-organized young scientists who wish to extend their knowledge and research experience in a structured 3-year PhD program, in order to pursue a successful career in cognitive neuroscience, clinical neuroscience, or neurophysics. The school is intended for students holding an excellent master's degree (or equivalent) in a wide spectrum of potential disciplines such as cognitive neuroscience, psychology, medicine, neurobiology, linguistics, computer science, engineering, mathematics, physics, biochemistry, or related fields. The university degree should be awarded by an internationally recognized university-level institution. Students near the completion of their master’s degree are also eligible to apply. Research experience in an area that is related to the graduate school’s scope is essential for successful candidates. Proficiency in oral and written English is mandatory. The IMPRS NeuroCom offers its doctoral students outstanding research opportunities in a very international and multidisciplinary environment with access to state-of-the-art cognitive and imaging neuroscience equipment, e.g. 7T MRI scanner, four 3T MRI scanners including a “connectome scanner” equipped with ultrastrong gradients (one of only three world-wide), a 306 channels MEG system, several TMS, TDCS, NIRS, and EEG systems. Applications will be evaluated by IMPRS NeuroCom faculty members. Interview selection is based on academic qualifications, personal references, research experience and interests, and suitability to the program. The Max Planck Society is an equal opportunity employer and is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. Payment is based on the guidelines of German public service pay scale (TVöD). For more information about our graduate school please visit: http://imprs-neurocom.mpg.de/home/ Please see http://imprs-neurocom.mpg.de/home/applications for details and use http://imprs-neurocom.mpg.de/home/applications/how-to-apply/registration-fo… for your application. For further information please contact Dr Veronika Krieghoff: vkrieghoff(a)cbs.mpg.de -- ************************************************************************** Prof. Dr. Martin Bogdan Institut für Informatik Technische Informatik Universität Leipzig Augustusplatz 10 D-04109 Leipzig Germany ************************************************************************** Denken Sie selbst, sonst tuen es Maschinen für Sie! 'Nihil est ab omni parte beatum' (Horaz) El problema de la humanidad es que los estúpidos están seguros de todo y los inteligentes están llenos de dudas **************************************************************************

1 0

Research Fellow in Computational Neuroscience, University of Warwick, UK
by Timofeeva, Yulia Nov. 6, 2019

Nov. 6, 2019

Research Fellow in Computational Neuroscience Department of Computer Science, University of Warwick, UK Fixed Term Contract for 3 years from 1 January 2020. The appointee will work on a project funded by the MRC that aims to develop and implement a mechanistic modelling framework for studying regulation of synaptic transmitter release in health and disease. This project will be led by Dr Yulia Timofeeva with the co-applicant Prof Kirill Volynski (UCL Queen Square Institute of Neurology, London) and in close collaboration with a number of world-leading experimental laboratories working in the field of synaptic transmission and information processing in the brain, that are located in Europe, USA, Canada and Japan. The successful candidate should have a PhD, or equivalent, in applied mathematics/theoretical physics/computer science or a related discipline and should have excellent skills in scientific computing. Previous experience of research in computational biology or neuroscience is desirable. The working environment will be in the Mathematical Science Building, in the Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER, https://warwick.ac.uk/fac/cross_fac/zeeman_institute/) For further details see https://www.dcs.warwick.ac.uk/~yulia/job_102287_109.html https://warwick.ac.uk/fac/sci/dcs/jobs/ Deadline for applications: 21 November 2019 -- __________________________________________ Dr Yulia Timofeeva Associate Professor Department of Computer Science and Centre for Complexity Science Warwick, UK Honorary Associate Professor UCL, Institute of Neurology London, UK Tel: 024 765 73786 http://www.dcs.warwick.ac.uk/~yulia/ __________________________________________

1 0

Assistant Professor position available in Cognitive Sciences at the University of California, Irvine
by Jeff Krichmar Nov. 5, 2019

Nov. 5, 2019

Dear Colleagues, We are accepting applications for an Assistant Professor position in Cognitive Sciences at the University of California, Irvine up until December 1st, 2019. The Department of Cognitive Sciences has a long history of combining a wide range of experimental methods with computational modeling at multiple levels. UCI is consistently recognized as a trailblazer in a broad range of fields, garnering national and international honors in every school. Please consider applying. The official job posting is below: The Department of Cognitive Sciences at the University of California, Irvine (UCI) invites applications for an assistant professor (tenure-track) position with an expected start date of July 1, 2020. We are seeking scientists who study learning, memory, decision making, and related topics with behavioral, developmental, computational, artificial intelligence, or neuroimaging methods. Of particular interest are cognitive scientists who combine an empirical research program with innovative quantitative analysis or computational modeling. The successful candidates will interact with a dynamic and growing community in cognitive, computational, and neural sciences within the department (http://www.cogsci.uci.edu/) and the broader campus. Interested candidates can find specific application requirements and the online application at: https://recruit.ap.uci.edu/JPF05668. To ensure full consideration, applications must be completed by December 1, 2019. The University of California, Irvine is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy. As a recipient of an NSF ADVANCE award for gender equity, UCI understands the needs of dual career couples, supports work-life balance through an array of family-friendly policies, and is dedicated to broadening participation in higher education. As a Minority Serving Institution, UCI seeks future faculty who will contribute to our enduring commitment to inclusive excellence and serve as role models. Best regards, 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

1 0

5 year PhD Interdisciplinary Neuroscience PhD Program, Tuebingen
by Peter Dayan Nov. 5, 2019

Nov. 5, 2019

The Max Planck Institute for Biological Cybernetics 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 ambition to shape the future of neuroscience and the ability to thrive in a fast-paced, interdisciplinary, environment. The application deadline is December 15, 2019. Please visit: https://www.kyb.tuebingen.mpg.de/phd-program for more details and information about applying. The PhD program is a collaboration between the Max Planck Institute for Biological Cybernetics 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 2020) 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.

1 0

Two PhD/Postdoc positions in theory of neuromorphic computing, Groningen, Netherland
by Herbert Jaeger Nov. 5, 2019

Nov. 5, 2019

In the group of Herbert Jaeger two fully funded positions are open for PhD students (4 year contract) or Postdocs (3 year contract). Both positions are about formal, theoretical analyses and algorithmic models of „neuromorphic“ computing in non-digital hardware (analog, unclocked, spiking microchips or even unconventional material substrates exhibiting relevant nonlinear dyanmical phenomena). Herbert Jaeger’s group is embedded in the Groningen Cognitive Systems and Materials Center (CogniGron, https://www.rug.nl/research/fse/cognitive-systems-and-materials/?lang=en) CogniGron, founded in 2018, is an interdisciplinary initiative at the intersection of computer science, AI, machine learning, computational neuroscience and material science. With 10 new professorships and 30 PhD stipends, CogniGron stands out as one of the most visible scientific investments in the Netherlands in recent times. The *first position* is defined within the European H2020 project „Memory technologies with multi-scale time constants for neuromorphic architectures (MeM-Scales)“, whose central objective is to build (analog, spiking) neuromorphic microchips which can adapt to online input signals which display several or even many timescales. Since microchip physics will deliver only a few physical timescales, collective computational phenomena will have to be explored in order to realize the long-range memory timescales required by many tasks. Since at this point, numerous but hardly explored options are "in the air" for computational timescale management, this position offers much freedom to engage in original work. The *second position* is funded through university budgets and is independent of specific project demands. The position holder will enjoy unusual freedom, paired with intellectual risk, to contribute to the ultimate scientific goal of Jaeger’s group: a unifying formal theory of information processing in nonlinear dynamical systems - regardless of whether they are similar to biological brains, or rest on non-neural dynamical phenomena in novel material substrates. Obviously, such a unifying theory, which would play for neuromorphic computing a similarly central role as Turing computability theory plays for digital computing, is not in sight and may be even not possible. However, many mini-revolutions in mathematical description formats are possible, and needed. Each position will be filled by either a PhD student with a 4-year contract, or by a Postdoc with a 3-year contract. The only selection criterion is qualification (product of intellectual audacity, analytical thinking power, and relevant mathematical and factual knowledge). Groningen is a beautiful and welcoming city, the university sits in the top 100 in virtually all global ranking lists, and the salary is highly competitive. More detail can be found in the official job announcements on the website of the University of Groningen: First position: https://www.rug.nl/about-us/work-with-us/job-opportunities/?details=00347-0… (PhD version) https://www.rug.nl/about-us/work-with-us/job-opportunities/?details=00347-0… (Postdoc version) Second position: https://www.rug.nl/about-us/work-with-us/job-opportunities/?details=00347-0… (PhD version) https://www.rug.nl/about-us/work-with-us/job-opportunities/?details=00347-0… (Postdoc version) Please apply for at most one of these formal job announcements, following the instructions given at these weblinks. For pre-application inquiries please contact me directly by email (h.jaeger(a)rug.nl) Applications received before December 1 will be given full consideration; however, the positions will remain open until filled. The earliest (and desirable) starting date for both positions is January 1, 2020. -- Dr. Herbert Jaeger Professor of Computing in Cognitive Materials Rijksuniversiteit Groningen Faculty of Science and Engineering - CogniGron Bernoulliborg Nijenborgh 9, 9747 AG Groningen web: minds.jacobs-university.de

1 0

Open position: MIT, Co-instructor and education support coordinator in computational neuroscience
by Ila Fiete Nov. 5, 2019

Nov. 5, 2019

Dear Colleagues, I would appreciate if you would pass along to appropriate candidates the following advertisement for an open position for a Co-instructor and education support coordinator in computational neuroscience at MIT. Apologies if you receive multiple postings. Best wishes, Ila Fiete ------------------------------------------------ COMPUTATION COURSE CO-INSTRUCTOR AND EDUCATION SUPPORT COORDINATOR, MIT Brain and Cognitive Sciences, to support the development and instruction of computational courses (85%) and provide assistance to the department as a whole on enhancing and evaluating the quality of its undergraduate course offerings (15%). The goal will be to integrate computational thinking skills across the Course 9 curriculum and in the new Computation and Cognition (Course 6-9) curriculum, and provide innovative training in the areas of computational neuroscience, neuroengineering, and human and machine intelligence. The main responsibility will be to develop learning content for MIT students in these areas, including instructional videos, tutorials, problem sets, demonstrations of basic neuroscience and data analysis methods. Will hold office hours and give in-class lectures as appropriate and provide feedback and guidance before and after a course launches to ensure a high-quality learning experience. Will also provide support to the department in enhancing and evaluating the undergraduate program broadly, including assisting with website content (e.g., videotapes of classroom instruction, faculty/student interactions, etc.) and coordinating with the Teaching and Learning Laboratory to evaluate the efficacy of the department’s approaches to improving undergraduate education; and perform other duties as requested. Job Requirements REQUIRED: Ph.D. in neuroscience, bioengineering, computational cognitive science or related/equivalent area; at least one year of teaching experience; proficiency with MATLAB and Python; excellent communication skills; and a demonstrated commitment to undergraduate education. Web publishing experience a plus; as is knowledge of Dreamweaver, Photoshop, InDesign, Fetch, and HTML coding. Job #17993. Link: https://careers.peopleclick.com/careerscp/client_mit/external/jobDetails/jo…

1 0

Data Scientist Position at Boston University
by Chen, Jerry Nov. 5, 2019

Nov. 5, 2019

The Lab of Jerry Chen at Boston University is hiring a Data Scientist to be involved in several multi-year BRAIN Initiative related NIH and NSF funded projects. These projects focus on understanding cortical computation during behavior by combining large-scale population recordings, anatomical reconstructions, and transcriptional profiling as well as developing tools for large-scale and high-speed imaging of neuronal populations. This person will be involved in help to analyze experimental data, developing software tools to aid in the data analysis, and helping with data infrastructure and management. Specific Projects include: 1. Analysis of dense electron microscope reconstructions of neuronal connectivity (ie. Connectomics) 2. Establishing pipeline for image analysis for in situ sequencing of gene expression 3. Establishing pipeline for automated behavioral training and analysis. 4. Visualization and analysis of population imaging data across multiple brain areas during behavior. This person will be jointly involved and mentored by personnel from the Hariri Institute's Software & Application Innovation Lab (SAIL), a center with expertise in cutting-edge computational and data-driven research with tangible and direct impacts on academic research, public service, and industry partners in healthcare, finance, and technology. Qualifications: BA/BS degree (MA or PhD preferred) in Computer Science, Mathematics, Engineering, Neuroscience or related technical field. One to three years of academic or professional experience. Programming experience in MATLAB is required. Additional experience in Python, C++, or LABView is preferred. Extensive background in either computational neuroscience, image analysis, computer vision, or machine learning is preferred. If interested in applying, please submit a CV along with 3 references to jerry(a)chen-lab.org<mailto:jerry@chen-lab.org>.

1 1