- Comp-neuro - lists.cnsorg.org

10th European Conference on Mathematical and Theoretical Biology

by Stephen Coombes

========== ECMTB/SMB 2016 - www.ecmtb2016.org<http://www.ecmtb2016.org> ========== ========== Call for Minisymposium proposals - deadline, 18 Dec 2015 ========== 10th European Conference on Mathematical and Theoretical Biology The joint meeting of the European Society for Mathematical and Theoretical Biology (ESMTB) and the annual meeting of the Society for Mathematical Biology (SMB) will be held in Nottingham, 11-15 July 2016. We now invite proposals for minisymposia at the interface of mathematics and biology, including all areas of the life and medical sciences. Minisymposia will be held in two-hour blocks, consisting of 4 talks of 30 minutes each (including time for questions and changing speakers). Please fill in the form at www.ecmtb2016.org/submissions/<http://www.ecmtb2016.org/submissions/> to submit your minisymposium proposal. Following submission, the minisymposium proposer will receive a unique link which they should forward to each speaker, in order to register and submit their individual abstracts. Minisymposium proposers are encouraged to consider geographical and gender diversity when selecting speakers. Submission of abstracts for contributed talks and posters will open in due course, with a deadline of 14 Feb 2016. Please note: The first submission associated with your email address will create a user account, and a password will be emailed to that email address. Each registered user may make a maximum of two submissions to ECMTB 2016 (one as a minisymposium organiser; one for a minisymposium talk, contributed talk or poster). =========== Confirmed plenary speakers include: ============ Ruth Baker (University of Oxford, UK) Sander van Doorn (University of Groningen, Netherlands) Julia Gog (University of Cambridge, UK) Leah Keshet (University of British Columbia, Canada) Johan van de Koppel (Royal Netherlands Institute for Sea Research) Hisashi Ohtsuki (Kanagawa, Japan) Johan Paulsson (Harvard University, USA) and John Rinzel (NYU, USA) - SMB Winfree Prize lecture ========== ========== ========== ========== ========== best wishes, Markus Owen (Chair of the Local Organising Committee, ECMTB/SMB 2016) Local Organising Committee: Markus Owen, Daniele Avitabile, Leah Band, Bindi Brook, Stephen Coombes, Etienne Farcot, John King, Reuben O'Dea, Ruediger Thul, Jonathan Wattis Scientific Committee: Linda Allen, Ellen Baake, Jim Cushing, Andreas Deutsch, Odo Diekmann, Susanne Ditlevsen, Stephen Eglen, Amina Eladdadi, Yoh Iwasa, Eva Kisdi, Santiago Schnell, Artie Sherman, Jonathan Sherratt, Vitaly Volpert 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 send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

Sept. 28, 2015

4th Winter Q-Bio Mtg in HAWAII Feb. 2016 ***Abstract submission deadline NOV. 10, 2015***

by Santamaria, Cookie

THE FOURTH ANNUAL WINTER Q-BIO MEETING Quantitative Biology on the Hawaiian Islands February 15-18, 2016 http://w-qbio.org/ The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. Technology is driving revolutionary changes in biology. Systems Biology has arisen as the deduction of interaction networks from -omics data generated in the wake of remarkable technological achievements. Likewise, DNA synthesis technologies are driving the development of Synthetic Biology, whereby engineered circuitry and even entire genomes can be reconstituted from chemical building blocks. These two emerging areas have catalyzed the growth of Quantitative Biology, whereby the central goal is the deduction of quantitative principles that can be used to construct predictive models for biological phenomena. The venue for 2016 is the Sheraton Waikiki<http://www.sheraton-waikiki.com/>, which is located in Honolulu, on the island of Oahu. The resort is known for its breathtaking oceanfront views, a first-of-its-kind recently opened "Superpool" and many award-winning dining venues. This year we will select contributed talks from the submitted abstracts to be presented with the invited talks during the plenary sessions. Contributed talks will also be selected for parallel breakout sessions that commence in the late afternoon. 2016 CONFIRMED SPEAKERS: Nathalie Balaban — Hebrew University Karen Carniol — Cell Hana El-Samad — UCSF James Ferrell — Stanford Justin Gallivan — DARPA Susan Golden — UCSD Jeff Hasty — UCSD Evonne Kaplan-Liss — Stony Brook Jennifer Lippincott-Schwartz — NIH X. Shirley Liu — Harvard Katie Pollard — UCSF Bryan Ray — Science Jonathan Weissman — UCSF Lingchong You — Duke CONFERENCE ORGANIZERS: Jeff Hasty, University of California, San Diego Galit Lahav, Harvard University Wendell Lim, University of California, San Francisco Gurol Suel, University of California, San Diego Olga Troyanskaya, Princeton & Simons Center for Data Analysis Lev Tsimring, University of California, San Diego ***REGISTRATION OPENS SOON! *** Registration fee covers conference venue, registration reception, banquet, coffee & snacks. EARLY BIRD REGISTRATION ($700 / $475 Student) DEADLINE: Sunday, December 20, 2015 REGULAR REGISTRATION ($800 / $575 Student) DEADLINE: Sunday, January 31, 2016 LATE REGISTRATION ($875 / $650 Student) After Sunday, January 31, 2016 REGISTRATION WILL BE AVAILABLE AT: http://w-qbio.org/ HOTEL: A block of rooms has been reserved for registered conference participants at the Sheraton Waikiki<http://www.sheraton-waikiki.com/> at a negotiated rate starting at $229 per night plus tax. We have also reserved a block of rooms at the Sheraton Princess Kaiulani<http://www.princess-kaiulani.com/> (just one block east and across the street from the Sheraton Waikiki) at a negotiated rate starting at $160 per night plus tax. The rooms will be available soon on a first-come, first-served basis, so book early! CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 10th deadline. Abstract guidelines and submission information at: http://www.w-qbio.org/submit-abstract/ ABSTRACT DEADLINE: Tuesday, November 10, 2015 Abstract guidelines and submission information at: http://www.w-qbio.org/submit-abstract/ We encourage you to forward this message to any colleagues who may be interested in taking part in this exciting event. Questions should be emailed to: coordinator(a)w-qbio.org<mailto:coordinator@w-qbio.org> SPONSORED BY: ACS Synthetic Biology UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology UC San Diego Divisions of Biological Sciences, Physical Sciences, q-bio, and Engineering

Sept. 28, 2015

Release of NEST 2.8.0

by Jochen Martin Eppler

Dear NEST users, NEST 2.8.0 is distributed under the GNU General Public License version 2 (or later). This version marks the completion of our development efforts during the HBP ramp up phase and consists of 290 repository checkins by 25 developers since 2.6.0. The most notable changes are: * The new connection framework introduced in NEST 2.6.0 can now handle parameter arrays for the 'all-to-all' and 'one-to-one' rules. * A new propagator for integrate-and-fire neurons correctly handles the case where membrane and synapse time constants are similar or the same. * Better documentation and much extended examples for PyNEST improve the discoverability of NEST's features. All users are encouraged to upgrade and adapt their simulation scripts to the changes in the user interface at this point in time to benefit from the improvements in the new version. For a full list of changes and download links, see https://github.com/nest/nest-simulator/releases/tag/v2.8.0 IMPORTANT: some of the defaults in NEST changed. You might have to adapt your scripts accordingly. See the release notes for details. Best regards, Jochen! -- Dr. Jochen Martin Eppler Phone: +49 2461 61-9471 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Sept. 27, 2015

Open position: Software Developer in Neuroinformatics

by Thomas Wachtler

At the German Neuroinformatics Node (G-Node, http://www.g-node.org) Ludwig-Maximilians-Universität München, a full-time position is available to join the G-Node team in developing neuroinformatics solutions for data management in neurophysiology. Variety and complexity of data in this field challenge large-scale data access, consistent storage and efficient data analysis. G-Node is interacting closely with research labs to address these challenges with state of the art neuroinformatics methods, including tools and formats for data annotation, management, and sharing. G-Node is funded by the Federal Ministry of Education and Research (BMBF) and is part of the Bernstein Network Computational Neuroscience (http://nncn.de) and national node of the International Neuroinformatics Coordinating Facility (INCF, http://incf.org) The position involves working in a small team of developers within a lively neuroscience environment, with ample opportunities for bridging between neuroscience research and neuroinformatics. Tasks include contributing to the development and enhancement of G-Node formats, tools and services (http://www.g-node.org/tools-and-services, https://github.com/G-Node) working closely with neuroscience laboratories that use, or plan to use, neuroinformatics solutions. Candidates should have excellent programming skills, preferably in Python and C++ or Java, the ability to work in a team, and a strong interest in the development of novel open-source solutions for neuroscience. Experience in fields of relevance, such as semantic web technologies, relational databases, web development, scientific software and analysis, experimental or computational neuroscience, would be beneficial. The position is available immediately, salary level is according to TV-L, duration is one year with possibility of extension. Individuals with disabilities will be given preference in case of equal qualification. Applications by women are specifically encouraged. Applications should include CV, statement of experience and motivation, and names of referees. Informal inquiries prior to application are welcome. Applications will be accepted until the position is filled. Applications should be sent, preferably as single pdf file by email, to Thomas Wachtler <wachtler(a)bio.lmu.de> -- Dr. Thomas Wachtler <wachtler(a)bio.lmu.de> Scientific Director German Neuroinformatics Node Department Biology II Ludwig-Maximilians-Universität München Grosshaderner Str. 2 82152 Planegg-Martinsried Germany

Sept. 26, 2015

Postdoctoral Position in Brain Mapping / Computational Neuroscience

by Stepanyants, Armen

The Neurogeometry Lab of Prof. Armen Stepanyants at the Department of Physics, in collaboration with the BIG-DATAbase group of Prof. Mirek Riedewald at the College of Computer and Information Science, Northeastern University, Boston, invite applicants for a postdoctoral position in Brain Mapping / Computational Neuroscience to begin in the fall of 2015. The successful candidate will work on an NIH sponsored project to develop algorithms and software tools for large-scale automated reconstruction of neurons from stacks of light microscopy images. Applicants should have a Ph.D. in mathematics, physics, electrical engineering, computer science, or related quantitative disciplines. Track record of experience in image processing, as well as excellent programming skills in Java and MatLab are essential. Knowledge of computer vision and machine learning algorithms is a plus. To apply, please send (1) a CV, including a list of publications, (2) a summary of prior research accomplishments, and (3) names and contact information of three reference providers by email to Prof. Armen Stepanyants, a.stepanyants(a)neu.edu<mailto:a.stepanyants@neu.edu>. The position is available immediately, and applications will be accepted until the position is filled. The initial appointment is for one year with the possibility of renewal on a yearly basis. Northeastern is an Equal Opportunity/Affirmative Action Title IX Employer. More information can be found at the Neurogeometry Lab website, www.neurogeometry.net<http://www.neurogeometry.net>. Armen Stepanyants Associate Professor Department of Physics and Center for Interdisciplinary Research on Complex Systems Northeastern University 110 Forsyth St., Boston, MA 02115 Phone: (617) 373-2944 Fax: (617) 373-2943 http://www.neurogeometry.net/

Sept. 25, 2015

News for Brain States: Characterization and Neuromodulation by DBS‏

by neuro girl

****News for Brain States: Characterization and Neuromodulation by DBS**** Abstract submission ends Sunday, September 27, 2015 at midnight EST. Registration is now open but space is limited. Please register now to secure your spot. Registration includes breakfast, coffee breaks and lunch. Information for submission and registration can be found at http://bit.ly/1JVElkf and https://dbs.veomed.net/. The Brain States: Characterization and Neuromodulation by DBS conference will take place on November 11-13, 2015 in Cologne, Germany. This is an interdisciplinary meeting with leading experts in academia and medicine who will present physiological, computational and clinical approaches to the brain dynamics and brain mechanics of complex functional networks in the brain. Transformations of the neurodynamic operations of the brain between the normal to the pathological state will be explored using multivariate data analysis (EEG, MEG, DBS, etc…). Special attention will be given to next-generation approaches which allow the collaboration of clinical practice and science to advance the field from principles of organization to the causal control of function. ********************************************************************************* Brain States: Characterization and Neuromodulation by DBS November 11-13, 2015 Cologne, Germany ******************************************************************************** We are proud to present a unique combination of internationally renowned speakers in an intimate setting which encourages open discussion. You are cordially invited to participate. Confirmed Speakers: Hagai Bergman (Hebrew University of Jerusalem) Peter Brown (University of Oxford) Stephan Chabardes (University Hospital Grenoble) Alain Destexhe (CNRS) Emad N. Eskandar (Massachusetts General Hospital-Harvard Medical School) Martijn Figee (University of Amsterdam) John J. Foxe (Albert Einstein College of Medicine) Marc Goodfellow (University of Exeter) Anthony A. Grace (University of Pittsburgh) Rowshanak Hashemiyoon (University Hospital of Cologne) Jens Haueisen (Technische Universität Ilmenau) Viktor Jirsa (Aix-Marseille Université /CNRS) Jens Kuhn (University Hospital Cologne) Klaus Lehnertz (University of Bonn) Andres Lozano (University of Toronto) Cameron McIntyre (Case Western Reserve University) Christoph M. Michel (University of Geneva) Urs Ribary (Simon Fraser University) Günter Schiepek (Paracelsus Medical University) Wolf Singer (Max Planck Institute for Brain Research) Dimitri van de Ville (University of Geneva) Veerle Visser-Vandewalle (University Hospital of Cologne) Jürgen Voges (Otto-von-Guericke-University Magdeburg) Looking forward to seeing you in Cologne! With kind regards, Row Hashemiyoon Rowshanak Hashemiyoon, PhD Chief, Behavioral Neurophysiology and Computational Neuroscience Klinik für Stereotaxie und Funktionelle Neurochirurgie Universitätsklinikum Köln Kerpener Str. 62 D - 50937 Köln Email: row.hashemiyoon(a)uk-koeln.de http://www.uk-koeln.de/de/stereotaxie

Sept. 25, 2015

Sainsbury Wellcome Centre Fellowships

by Peter Dayan

Under the Directorship of Professor John O’Keefe, the Sainsbury Wellcome Centre for Neural Circuits and Behaviour (SWC) will bring together world-leading scientists to investigate how brain circuits process information to create the neural representations that guide behaviour. Developed through the vision and partnership of the Gatsby Charitable Foundation and the Wellcome Trust, and with substantial investment from these partners, the mission of SWC is to transform understanding of brain function. The Centre, located within UCL and close to its main campus in central London, is being structured to foster a culture of innovation, collaboration, enquiry and excellence. SWC scientists will use the latest advances in molecular and cellular biology, imaging, electrophysiology and behavioural techniques and enjoy an unparalleled research environment offering state-of-the-art research laboratories, cutting-edge scientific equipment, technologically-advanced prototyping and fabrication laboratories and custom in-house high-performance computing facilities. Commencing research operations in early 2016, SWC will comprise 12 highly interdisciplinary experimental research groups accommodated in a new, purpose-designed, seven-storey building. The Gatsby Computational Neuroscience Unit has relocated to the new building, facilitating broad and deep collaborations in data analysis and computational modelling. Scientists joining SWC will become part of UCL Neuroscience which brings together over 450 principal investigators offering extensive opportunities for interaction and collaboration. Formal teaching commitments will be minimal allowing scientists to focus on research. The Centre invites applications for SWC Senior and Principal Research Fellowships from outstanding, innovative, highly-motivated collaborative scientists with backgrounds in neuroscience as well as related physical and biological sciences. It is particularly interested in scientists wishing to extend the boundaries of technological development in areas such as high- density electrophysiological probes, telemetry, optical recording, molecular and genetic tools, new anatomical mapping techniques, and the use of virtual reality and other novel behavioural approaches such as video image analysis. Competitive salaries, tailored research space and generous relocation and recruitment packages, including research support, will be offered. Shortlisted fellowship candidates will be invited to a residential recruitment symposium scheduled for 18-20 November 2015. For further details, please visit: http://www.ucl.ac.uk/swc/opportunities Expressions of interest in senior academic positions are also welcome and may be addressed to the Centre Director or Centre Manager. Contact details are available on the web pages.

Sept. 24, 2015

Call for applications: travel grants for advanced PhD students, the 2016 ELSC Annual Retreat

by Yoram Burak

Dear Colleagues, Please distribute this to graduate students who might be interested. Sincerely, Yoram Burak --- The 2016 ELSC Annual Retreat January 24-26, Kibbutz Ein Gedi, Israel The Edmond and Lily Safra Center for Brain Sciences at the Hebrew University offers competitive scholarships to support the travel and accommodation of 20 outstanding advanced international Ph.D. students to present their work in our annual retreat. These scholarship are offered for the first time this year. ELSC is a multidisciplinary neuroscience center. Our retreat thus covers the whole spectrum of brain research, including computational, molecular, cognitive, and systems neuroscience. The ELSC retreat is an optimal venue for advanced Ph.D. students to present their work and receive expert feedback. The program includes talks by our advanced graduate students, and plenary speakers: Fred Wolf (MPI for Dynamics and Self Organization, Göttingen), Ilana Witten (Princeton University), and Serge Domoulin (Utrecht University). Candidates are requested to send their CV, a letter of intent, and a recommendation letter to BRAIN(a)ELSC.huji.ac.il by November 1st, 2015. Awardees will be announced no later than November 15th. See also: http://elsc.huji.ac.il/content/travel-grants-elsc-retreat ---

Sept. 24, 2015

Three postdoctoral positions in computational and systems olfactory neuroscience in Pittsburgh

by Nathan Urban

Drs. Bard Ermentrout and Nathan Urban of the University of Pittsburgh, (Departments of Mathematics and Neurobiology) and the Center for the Neural Basis of Cognition invite applications for three postdoctoral positions for a NSF-funded BRAIN initiative project focused on the experimental and computational analysis of odor-driven navigation. (See NSF press release: http://www.nsf.gov/news/news_summ.jsp?cntn_id=136333&org=NSF&from=news and http://www.nsf.gov/awardsearch/showAward?AWD_ID=1555862&HistoricalAwards=fa… ) This three year project involves investigators at six institutions and is focused on analysis of how olfactory cues are used to guide navigation behavior in a number of species. Both behavioral strategies and brain mechanisms will be evaluated. The Pittsburgh group will combine experimental and computational approaches and will integrate detailed measurement and analysis of mouse behavior with simultaneous measurements of neural activity. We seek candidates with expertise in: Neurophysiology especially in vivo recording Automated behavioral analysis Computational models of brain networks The successful candidate will have a PhD or equivalent degree in neuroscience, applied math, engineering, computer science or a related discipline. Successful candidates will have a track record of publications and experience in experimental and/or computational neuroscience. Postdocs will be expected to participate in ongoing collaborations with other groups in Pittsburgh and in other locations, especially the other members of this project team. Postdocs in the lab will have the opportunity to present their work at national and international meetings and to take advantage of many opportunities for professional development.. Applicants can contact Dr. Urban via e-mail at nurban(a)pitt.edu and/ or Dr Ermentrout at bard(a)pitt.edu and should apply via: *https://goo.gl/HkhtY5 <https://goo.gl/HkhtY5>.Nathan Urban, Ph.D.Vice Provost for Special Projects829 Cathedral of LearningProfessor and Associate Chair - Department of Neurobiologyhttp://www.neurobio.pitt.edu/ <http://www.neurobio.pitt.edu/>Co-Director Center for the Neural basis of Cognitionwww.cnbc.cmu.edu <http://www.cnbc.cmu.edu/>Associate Director Pittsburgh Brain Institutehttp://www.braininstitute.pitt.edu/ <http://www.braininstitute.pitt.edu/>E1440 BSTWR200 Lothrop StreetUniversity of PittsburghPittsburgh, PA 15213Phone: 412-648-3396nurban(a)pitt.edu <nurban(a)pitt.edu> *

Sept. 23, 2015

Announcing the first NESTML community workshop

by Jochen Martin Eppler

Announcing the first community workshop on NESTML, the novel modelling language to create neuron models for the NEST simulator for spiking neuronal networks (nest-simulator.org) Abstract ^^^^^^^^ Currently, neuron and synapse models in NEST are written as C++ classes. These classes implement the simulator API for updating the neuronal dynamics, sending and receiving events, and auxiliary tasks such as initialization, recording of internal variables, calibration and handling of parameters. As the model code is hand-written and often created by copy and paste, this method is prone to errors and hinders the programmatic re-use of components such as neuronal dynamics, post-synaptic responses and synaptic plasticity mechanisms. Moreover, as many neuroscientists are not experts in C++, the process of creating models is often seen as complicated and in many cases the resulting model implementations are not optimal with respect to performance, consistency and testability. To ease writing models for NEST and improve the general quality of the code, we have created the NEST Modelling Language. NESTML comprises a language specification to describe neuron models in terms of neuroscience concepts and a set of tools to generate efficient C++ code for NEST from this description. During the workshop, we will give a general introduction to model creation for NEST and an in-depth introduction to the concepts and application of NESTML. In hands-on sessions the participants have the opportunity to write their own models in NESTML with the assistance of experienced tutors. The feedback collected in a dedicated session will be used to shape the future design and development of NESTML. Target Audience ^^^^^^^^^^^^^^^ The workshop aims at students and researchers in computational neuroscience who want to create their own neuron models in NEST. Some understanding of programming and experience with one of the simulators NEST, NEURON, or Brian will be helpful, but are not strictly required. Location and date ^^^^^^^^^^^^^^^^^ The workshop will take place at the Chair of Software Engineering (se-rwth.de) of RWTH Aachen University from Monday, December 7 to Wednesday, December 9, 2015. Details and registration Workshop attendance is possible free of charge. However, in order to be able to plan rooms, lunches and coffee breaks, we require registration. For details and enrolment, visit www.fz-juelich.de/ias/jsc/nestml-ws. With best regards, Jochen! -- Dr. Jochen Martin Eppler Phone: +49 2461 61-9471 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

Sept. 23, 2015