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Publication of the book "Computational Glioscience"
by Maurizio De Pitta Jan. 27, 2019

Jan. 27, 2019

Dear colleagues, I would like to share with you the news of the publication of the book entitled "Computational Glioscience" (Springer, 2019). The book, which is co-edited by who is writing in collaboration with Dr. Hugues Berry (Inria, France) showcases a collection of original chapters In addition, feel free to reach out authors of individual chapters independently to ask for a copy of their manuscript if needed, that are authored by a pool of more than thirty internationally-renowned scientists. In particular, the book aims at presenting a selection of recent modelling approaches on the complex, emerging topic of neuron-glial interactions, from subcellular to network levels, both for experts and non-experts in the field. The whole book along with individual chapters may be accessed at the following link: https://link.springer.com/book/10.1007/978-3-030-00817-8 A repository with freely-downloadable code used in the simulations of the book is also available at the address below: https://github.com/mdepitta/comp-glia-book The following is the Table of Contents of the book: Part I -- Introduction 1. M. De Pittà and H. Berry, A Neuron–Glial Perspective for Computational Neuroscience Part II -- Calcium Dynamics 2. I. Siekmann, P. Cao, J. Sneyd and E. J. Crampin, Data-Driven Modelling of the Inositol Trisphosphate Receptor (IP3R) and its Role in Calcium-Induced Calcium Release (CICR) 3. Y. Timofeeva, Intracellular Calcium Dynamics: Biophysical and Simplified Models 4. S. Rüdiger and J. Shuai, Modeling of Stochastic Ca2+ Signals 5. M. De Pittà, E. Ben-Jacob and H. Berry, G Protein-Coupled Receptor-Mediated Calcium Signaling in Astrocytes 6. V. Matrosov, S. Gordleeva, N. Boldyreva, E. Ben-Jacob, V. Kazantsev and M. De Pittà, Emergence of Regular and Complex Calcium Oscillations Inositol 1,4,5-Trisphosphate Signaling in Astrocytes 7. J. Lallouette, M. De Pittà and H. Berry, Astrocyte Networks and Intercellular Calcium Propagation Part III -- Tripartite Synapse and Regulation of Network Activity 8. C. González-Arias and G. Perea, Gliotransmission at Tripartite Synapses 9. A. Pillai and S. Nadkarni, Purinergic Signaling at Tripartite Synapses 10. M. De Pittà, Gliotransmitter Exocytosis and Its Consequences on Synaptic Transmission 11. V. Volman and M. Bazhenov, Computational Models of Pathophysiological Glial Activation in CNS Disorders Part IV -- Homeostasis and Metabolic Coupling 12. A. Scimemi, The Role of Astrocytes in Neurotransmitter Uptake and Brain Metabolism 13. K. Mergenthaler, F. Oschmann and K. Obermeyer, Glutamate Uptake by Astrocytic Transporters 14. G. Halnes, K. H. Pettersen, L. Øyehaug, M. E. Rognes and G. T. Einevoll, Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow 15. T. Çakır, Constraint-Based Modeling of Metabolic Interactions in and Between Astrocytes and Neurons Part V -- Computational Tools to Analyze and Model Astrocyte Experiments 16. T. Manninen, R. Havela and M.-L. Linne, Computational Models of Astrocytes and Astrocyte–Neuron Interactions: Characterization, Reproducibility, and Future Perspectives 17. S. Venugopal, R. Srinivasan and B. S. Khakh, GECIquant: Semi-automated Detection and Quantification of Astrocyte Intracellular Ca2+ Signals Monitored with GCaMP6f 18. M. Stimberg, D. F. M. Goodman, R. Brette and M. De Pittà, Modeling Neuron–Glia Interactions with the Brian 2 Simulator In addition, feel free to independently reach out the authors of individual chapters to ask for a copy of their manuscript if needed. Please disseminate the news among your team members, students and colleagues. Thank you for your consideration of the matter. Sincerely, Maurizio De Pitta' ----- 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

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PhD IN INTERDISCIPLINARY NEUROSCIENCE @ LISBON
by Prata, Diana Jan. 26, 2019

Jan. 26, 2019

A PhD IN INTERDISCIPLINARY NEUROSCIENCE AND IN LISBON? Go to: https://www.neurulisboa-phd.com/. You can visit our lab’s page to choose a project theme around oxytocin’s role in social cognition using neuroimaging/EEG/pupilometry/SCR, or psychiatric multimodal biomarkers), dpratalab.wordpress.com<http://dpratalab.wordpress.com>, contact the PI; and apply for a NeurULisboa fellowship (deadline 14th of February). Diana Prata, Phd Marie Curie Fellow Principal Investigator (Biomedical Neuroscience Lab), Instituto de Biofísica e Engenharia Biomédica, FCUL Visiting Lecturer, IoPPN, King's College London

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Job advert / 3 year post-doc LMU Munich computational social neuroscience
by Deroy, Ophelia Jan. 25, 2019

Jan. 25, 2019

We are looking for One Post-Doctoral Research Fellow in Computational Social Neuroscience for 3 Years, to be based at the LMU, Munich. The expected starting date is between April 1st, 2019 and July 1st, 2019 Deadline for applications is February 15th, 2019 This post-doctoral fellowship will investigate how the diversity of social information affects attitudes and decisions, both for individuals and groups. This post is part of a broader project supported by the NOMIS foundation to apply quantitative methods (behavioural, computational and neuroimaging) to examine - under controlled and ecologically-valid settings - fundamental issues on the impact of diversity and volatility of information on social influence. The project is hosted by the Munich Centre for Neuroscience, and will be supervised Professor Ophelia Deroy and Dr. Bahador Bahrami. International collaborations (with Gatsby Computational Neuroscience Unit, University College London as well as Centre for Adaptive Rationality in Max Planck Institute for Human development in Berlin) are integral to the project and the current position. Job Description: The appointee will be expected to - develop research ideas and plan and implement experiments (ethics, design, programming); - conduct experiments and collect data from adult human subjects; - perform statistical analysis (with particular focus on using computational modelling to - prepare reports and articles for publication; - participate in regular meetings and contribute to the research environment; - supervise research assistants - work as part of a team. Requirements: The successful candidate will have a PhD level - a strong background in quantitative methods (statistics, physics, machine learning, computational neuroscience) - interest in interdisciplinary projects and - a PhD in computer sciences (machine learning), physics (eg complex systems), psychology (cognitive or social), or neuroscience (behavioural, systems). Knowledge of experimental design, statistics and data analysis is expected. Strong command of linear algebra, probability theory, computer programming (web-based platforms (e.g. Java), R, Python, Matlab) is highly desirable. The position is for three years, with an intermediate evaluation for satisfactory performance after 1 year. The appointment will be made within the German TV-L E 14 salary scheme (family benefits apply). Applications should include a CV (including full list of publications and skills), cover letter and the contact details of three referees. Address for preliminary information and applications: bahador.bahrami(a)lmu.de

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Postdoctoral position jointly in Behrmann/Grover labs CMU in understanding neural mechanisms through noninvasive brain monitoring
by Pulkit Grover Jan. 25, 2019

Jan. 25, 2019

Postdoctoral position jointly in Behrmann/Grover labs CMU in understanding neural mechanisms through noninvasive brain monitoring A postdoc position on utilizing noninvasive measurement modalities is available in the labs of Marlene Behrmann and Pulkit Grover at Carnegie Mellon University (Pittsburgh, PA). The team's goal is to utilize existing and novel engineering and mathematical tools to understand neural mechanisms in healthy and diseased states through EEG measurements, possibly complemented by fMRI. The role of the postdoc will be to lead experimental testing, simulations, and data analysis. The postdoc will collaborate with information theorists, neuroscientists, experimentalists, and clinicians. This is an opportunity to work on challenging and applicable scientific problems in a highly interdisciplinary and vibrant environment. Requirements: PhD in a related discipline (Engineering, Computer Science, Neuroscience, or Biomedical Engineering) with a strong experimental and computational record. Background in EEG recordings is required. The labs are committed to the professional development of the members, making this position a valuable preparation for those interested in academic, industrial or entrepreneurial careers. The position has no mandatory teaching or administrative duties. The ideal start date is April 2019, but early applications will also be accepted. The position is initially for 12 months with the possibility of renewal. Compensation will be competitive, and commensurate with relevant experience. Candidates should send a CV, a statement of research experience and interests, expected date of availability, and the contact information for three references to behrmann(a)cmu.edu and pulkit(a)cmu.edu with the subject line “neural monitoring postdoc”. Application review will proceed until the position is filled.

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Systems Neuroscience: a study abroad summer program
by Bányai Mihály Jan. 25, 2019

Jan. 25, 2019

Dear colleagues, I've been asked to circulate the announcement below on the comp-neuro list: Our Dear Colleagues: BSCS-US http://www.bscs-us.org/ announces a study abroad program in Budapest: Systems Neuroscience: a study abroad summer program Program start/end dates: June 10th - Aug 2d, 2019 The BSCS Systems Neuroscience Program takes place at and academically supervised by the Department of Anatomy, Histology and Embryology, Semmelweis University Medical School, Budapest. Transcript is issued by the Registrar of the Semmelweis University Medical School, and sent directly to the Registrar of your college/university. For details, see: http://sysneuro-semester.org/ [sysneuro-semester.org] Inquiry: Program directors / academic supervisors Péter Érdi perdi(a)kzoo.edu László Négyessy <negyessy(a)gmail.com> John Milton <JMilton(a)kecksci.claremont.edu> Office: bscs(a)bscs-us.org With kind regards, Péter Érdi http://people.kzoo.edu/~perdi/ aboutranking.com https://www.ijcnn.org/

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Job opening at Research Center Juelich - Coordinator Software Technology
by Martina Reske Jan. 25, 2019

Jan. 25, 2019

The Institute of Neuroscience and Medicine (INM) at the Jülich Research Center in Germany investigates the structure and function of the brain. The Subinstitute INM-6 consists of 4 departments and 1 team that conduct research in the field of computational and systems neuroscience. The Statistical Neuroscience group headed by Prof. Sonja Grün develops computational methods to analyze the joint activity of neuronal networks, and applies these methods to experimental data in the context of international collaborations using state-of-the-art approaches from neuroinformatics. For this project the Statistical Neuroscience group is seeking a Coordinator Software Technology Your Job: * Development, maintenance, and distribution of the Elephant analysis software (python-elephant.org) * Planning and coordination of software development for the Elephant software * Development of solutions for software packaging to bundle individual resources, including cross-language components of the software and deployment on large systems * Installation, provisioning, and adaptation of the software and matching environments on heterogeneous HPC systems * Management of open-source software development cycles using suitable agile paradigms, and handling inquiries and contributions via issue systems and similar channels * Review and evaluation of software contributions from a world-wide community with respect to scientific content, the code maturity, and the possibility to be integrated into the Elephant software * Guidance and coordination of the code review process * Co-design and dissemination of generic conceptual guidelines and project-specific implementations for scientific workflows, in close dialogue with scientists and developers and by incorporating current software developments * Implementing library features and statistical analysis tools for neuronal data * Parallelization of analysis codes using modern technologies * Actively contacting and supporting method developers * Maintenance of the software documentation and accompanying teaching material, including content for the presentation of the software on the web and on social media * Representing the technology at scientific conferences, during educational courses, to the public, and within the framework of the EU Flagship Project “Human Brain Project” Your Profile: * University degree in natural sciences, computer science or mathematics * Very good expertise in the programming language Python, as well as C/C++ or Matlab, in parallelization techniques (MPI, openMP,...) and in the standard Linux tools as well as web-based services for managing software (version control, issue tracking,…) * Experience in implementing scientific analysis methods * Experience in creating documentation and course material * High ability to work in an interdisciplinary, international team * Fluent in English, spoken and written * Ability to work independently, systematically and on one’s own responsibility * Good communication skills * Willingness to travel Our Offer: * A green campus with world-leading scientific infrastructure near the cultural centers of Cologne, Düsseldorf, and Aachen * A position in a creative and international team that conducts research at the frontiers of science, themes ranging from computational neuroscience to simulation technology * World class science environment at the interface between neuroscience and technology on the most complex known systems * Excellent scientific equipment including the fastest supercomputer in Europe * A comprehensive further training programme * Flexible working hours and various opportunities to reconcile work and family life * Limited until 31.03.2020 with possible longer-term prospects * Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD). Depending on the applicant's qualifications and the precise nature of the tasks, salary grade 13-14 TVöD-Bund Forschungszentrum Jülich aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. We look forward to receiving your application, preferably the online recruitment system on our career site, quoting the reference number 2018-321 at https://www.hrecruiting.de/obf2/bewerbermanagement.php?kunden_nr=t5ChjatkIf… -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> Office hours: TU & FR 9.00-17, WE & TH 9.00-13 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Job opening at Research Center Juelich - Data Manager
by Martina Reske Jan. 25, 2019

Jan. 25, 2019

The Institute of Neuroscience and Medicine (INM) at the Jülich Research Center in Germany investigates the structure and function of the brain. The subinstitute INM-6 consists of 4 departments and 1 team that conduct research in the field of computational and systems neuroscience. The Statistical Neuroscience department headed by Prof. Sonja Grün develops computational methods to analyze the joint activity of neuronal networks, and applies these methods to experimental data in the context of international collaborations using state-of-the-art approaches from neuroinformatics. For this project the Statistical Neuroscience group is seeking a Datamanager Your Job: * Development and maintenance of the data processing workflows of the institute using state-of-the-art technologies along the FAIR principles, including experimental recordings, simulation outcomes, and data produced by the analysis process * Design of metadata schemes for different work areas (experiments/simulation) * Development of concepts for interfacing data storage technologies with complementary software * Development of ontologies and software tools with the community * In-depth curation and documentation of primary data (e.g., spikes, LFPs or Ca2+ imaging) * Implementation of version-controlled, provenance-tracked data preprocessing pipelines and solutions for cross-lab data storage and exchange * Integration of primary data and metadata in the different work areas * Assisting scientists in the implementation of custom codes for data processing * Preparing datasets for publication and making data discoverable by knowledge graphs * Training lab members and collaborators in data management best practices * Representing the technology at scientific conferences and courses, to the public, and within the EU Flagship Project “Human Brain Project” Your Profile: * University degree in natural sciences or computer science * Good expertise in Python and Matlab, in semantic web technologies relevant for data curation, ontologies and provenance (RDF, XML, JSON, SHACL, PROV,…), in version control and issue tracking systems, and in Linux * Experience with electrophysiological data and corresponding acquisition/storage Technologies * Experience in web development * Experience in training and documentation * High ability to work in an interdisciplinary, international team * Fluent in English, spoken and written * Ability to work independently, systematically and on one’s own responsibility * Good communication skills * Willingness to travel Our Offer: * Exciting work setting on an attractive research campus with a very good infrastructure, ideally situated within the city triangle of Cologne, Düsseldorf, and Aachen * A position in a creative and international team that conducts research at the frontiers of science, themes ranging from computational neuroscience to simulation technology * World class science environment at the interface between neuroscience and technology on the most complex known systems * Excellent scientific equipment including the fastest supercomputer in Europe * A comprehensive further training programme * Flexible working hours and various opportunities to reconcile work and family life * Limited until 31.03.2020 with possible longer-term prospects * Salary and social benefits in conformity with the provisions of the Collective Agreement for the Civil Service (TVöD). Depending on the applicant's qualifications and the precise nature of the tasks, salary grade 13-14 TVöD-Bund Forschungszentrum Jülich aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. We look forward to receiving your application, preferably the online recruitment system on our career site, quoting the reference number 2018-322, https://www.hrecruiting.de/obf2/bewerbermanagement.php?kunden_nr=t5ChjatkIf… -- Dr. Martina Reske Scientific Coordinator Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience Jülich Research Centre and JARA Jülich, Germany Work +49.2461.611916 Work Cell +49.151.26156918 Fax +49.2461.619460 www.csn.fz-juelich.de<http://www.csn.fz-juelich.de> Office hours: TU & FR 9.00-17, WE & TH 9.00-13 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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PhD position: model-based analysis of atypical perception in autism
by Dominik Endres Jan. 24, 2019

Jan. 24, 2019

*Project title*: Atypical Perception in Autism-Spectrum Disorders: Model-based Analysis of Functional and MR-Spectroscopy Data for the Investigation of Deviant Perceptual Processes *What we offer*: A PhD student position in an interdisciplinary, DFG-funded research project, involving a combination of functional imaging, Psychiatry, and computational modeling. The position is part-time (65 % of regular working hours) with salary and benefits commensurate with a public service position in the state Hesse, Germany (TV-H E 13). An association with the DFG-RTG 2271 ‘breaking expectations’ or the CRC 135 ‘Cardinal Mechanisms of Perception’ is possible and encouraged. *What we expect*: a qualified degree in Neuroscience, Psychology, Cognitive Science, Computer Science, engineering or Physics (Master, Diploma, or comparable) as well as demonstrable programming experience in a high-level language, e.g. Python or Matlab. We expect you to be interested in the topic of the project (to be documented in a motivation letter (1 page max), in which you may refer to prior experiences, for instance, a thematically pertinent thesis, student research assistant positions, etc.), or quantitative modeling. We also expect prior exposure to machine learning and Bayesian statistics. *Application deadline*: 15.02.2019 Feel free to contact Prof. Dr. Dominik Endres at mailto:dominik.endres@uni- marburg.de for more information. The official advert can be found at https://www.uni-marburg.de/de/universitaet/administration/verwaltung/ dezernat2/personalabteilung/bewerber/stellen/wissenschaftliche-stellen/ fb04-0001-wmz-150219-englisch.pdf -- Prof. Dr. Dominik Endres AE Theoretische Neurowissenschaft Allgemeine und Biologische Psychologie FB Psychologie, Gutenbergstr 18, 35032 Marburg, Germany Tel. +49-(0)6421-28-23818

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Call for Paper: Scipy 2019 / Cognitive Science & Neuroscience
by Nicolas Rougier Jan. 24, 2019

Jan. 24, 2019

Dear all, We’re thrilled to announce the call for paper for the SciPy (Scientific Python) 2019 conference is open. You’ll find relevant information below. Olivia Guest & Nicolas Rougier Co-chairs for the Cognitive Science & Neuroscience symposia --- When: July 8, 2019 to July 14, 2019 (main conference from July 10 to July 12) Where: Austin, Texas, USA Who: The annual SciPy Conference brings together over 800 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. What: short summary (~100 words) + abstract (~500 words) Deadline: February 10, 2019 Conference Website: https://www.scipy2019.scipy.org/ Submission Website: https://easychair.org/conferences/?conf=scipy2019

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Fwd: Chief technologist position at Columbia University Medical Center
by Shivakeshavan Ratnadurai Giridharan Jan. 22, 2019

Jan. 22, 2019

Sent on behalf of Jason B. Carmel, CUMC. Please see message below. Thanks, Shiva _____________________________________________ We are seeking a Chief Technologist for the Movement Recovery Laboratory at Columbia University Medical Center. The successful candidate will have strong programming and neuroscience experience with expertise in signal processing and analysis of large data sets. The position is ideal for a person who likes to develop and optimize neuroscience tools. He or she will be responsible for creating and maintaining the systems for cutting-edge neuroscience research that seeks to restore movement after paralyzing injury. The Laboratory uses rodent models of disease to improve understanding of movement control, to test how electrical stimulation can strengthen neural circuits spared by injury. The laboratory uses a combination of behavior, physiology, and anatomy techniques in rats. Each of these modalities has a suite of tools that need to be made more quantitative, efficient, and precise. 1. Behavior: We quantify reaching, walking, and food manipulation using robotics and computer vision. The Chief Technologist will be charged with creating protocols and algorithms to efficiently record and analyze these movements, including reaching, stepping, and manipulation. 2. Physiology: We record and stimulate both motor cortex and the spinal cord. The technologist will help develop protocols for multichannel stimulation and for analysis of nerve and muscle signals. For example, we have created a graphical tool for real-time visualization of EMG responses to motor cortex stimulation. 3. Anatomy: We trace connections between the brain and the spinal cord using a combination of anterograde and retrograde neural tracers. The technologist will help quantify the number of labeled neurons and axons using computer vision and the results are placed into a 3D framework. The chief technologist will be expected to work independently to establish protocols and to help test them. This research work will require pro-active and interdisciplinary teamwork. The candidate should hold a PhD (or equivalent) in neuroscience, biomedical engineering, computer science, or a related field. Software design and programming skills in MATLAB (or equivalent scientific software) are critical. Knowledge of machine learning, computer vision, and source localization are other appealing skills. Most important is the ability to find innovative and practical solutions to technical problems. The position has a starting salary of $55,000 to $70,000, depending on experience, and includes full medical, dental, retirement, and other benefits. The position is supported by NIH, New York State, and private foundation grants. Columbia University is located in New York City, has a world-class faculty in neuroscience and neurology. Abundant learning opportunities include lab meetings, seminar series, journal clubs and university lectures. There are also many opportunities for collaboration with other neuroscientists, laboratories creating new technologies, and expert clinicians. Email your CV and cover letter (or inquiries) to Jason B. Carmel, MD, PhD at jason.carmel(a)columbia.edu. Please include “Chief Technologist” in the subject line. Columbia University takes Affirmative Action to ensure equal opportunity.

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