Thursday, January 31, 2013

[Comp-neuro] [ANN] Summer School "Advanced Scientific Programming in Python" in Zürich, Switzerland

Advanced Scientific Programming in Python
a Summer School by the G-Node and the Physik-Institut, University of Zurich

Scientists spend more and more time writing, maintaining, and
debugging software. While techniques for doing this efficiently have
evolved, only few scientists actually use them. As a result, instead
of doing their research, they spend far too much time writing
deficient code and reinventing the wheel. In this course we will
present a selection of advanced programming techniques,
incorporating theoretical lectures and practical exercises tailored
to the needs of a programming scientist. New skills will be tested
in a real programming project: we will team up to develop an
entertaining scientific computer game.

We use the Python programming language for the entire course. Python
works as a simple programming language for beginners, but more
importantly, it also works great in scientific simulations and data
analysis. We show how clean language design, ease of extensibility,
and the great wealth of open source libraries for scientific
computing and data visualization are driving Python to become a
standard tool for the programming scientist.

This school is targeted at Master or PhD students and Post-docs from
all areas of science. Competence in Python or in another language
such as Java, C/C++, MATLAB, or Mathematica is absolutely required.
Basic knowledge of Python is assumed. Participants without any prior
experience with Python should work through the proposed introductory
materials before the course.

Date and Location
September 1—6, 2013. Zürich, Switzerlandi.

Preliminary Program
Day 0 (Sun Sept 1) — Best Programming Practices
- Best Practices, Development Methodologies and the Zen of Python
- Version control with git
- Object-oriented programming & design patterns
Day 1 (Mon Sept 2) — Software Carpentry
- Test-driven development, unit testing & quality assurance
- Debugging, profiling and benchmarking techniques
- Best practices in data visualization
- Programming in teams
Day 2 (Tue Sept 3) — Scientific Tools for Python
- Advanced NumPy
- The Quest for Speed (intro): Interfacing to C with Cython
- Advanced Python I: idioms, useful built-in data structures, generators
Day 3 (Wed Sept 4) — The Quest for Speed
- Writing parallel applications in Python
- Programming project
Day 4 (Thu Sept 5) — Efficient Memory Management
- When parallelization does not help:
the starving CPUs problem
- Advanced Python II: decorators and context managers
- Programming project
Day 5 (Fri Sept 6) — Practical Software Development
- Programming project
- The Pelita Tournament

Every evening we will have the tutors' consultation hour : Tutors will
answer your questions and give suggestions for your own projects.

You can apply on-line at

Applications must be submitted before 23:59 CEST, May 1, 2013.
Notifications of acceptance will be sent by June 1, 2013.

No fee is charged but participants should take care of travel,
living, and accommodation expenses. Candidates will be selected on
the basis of their profile. Places are limited: acceptance rate is
usually around 20%. Prerequisites: You are supposed to know the
basics of Python to participate in the lectures. You are encouraged
to go through the introductory material available on the website.

- Francesc Alted, Continuum Analytics Inc., USA
- Pietro Berkes, Enthought Inc., UK
- Valentin Haenel, freelance developer and consultant, Berlin, Germany
- Zbigniew Jędrzejewski-Szmek, Krasnow Institute,
George Mason University, USA
- Eilif Muller, Blue Brain Project, École Polytechnique Fédérale de
Lausanne, Switzerland
- Emanuele Olivetti, NeuroInformatics Laboratory, Fondazione Bruno
Kessler and University of Trento, Italy
- Rike-Benjamin Schuppner, Technologit GbR, Germany
- Bartosz Teleńczuk, Unité de Neurosciences Information et Complexité,
CNRS, France
- Stéfan van der Walt, Applied Mathematics, Stellenbosch University,
South Africa
- Bastian Venthur, Berlin Institute of Technology and Bernstein Focus
Neurotechnology, Germany
- Niko Wilbert, TNG Technology Consulting GmbH, Germany
- Tiziano Zito, Institute for Theoretical Biology, Humboldt-Universität
zu Berlin, Germany

Organized by Nicola Chiapolini and colleagues of the Physik-Institut,
University of Zurich, and by Zbigniew Jędrzejewski-Szmek and Tiziano Zito for
the German Neuroinformatics Node of the INCF.


Wednesday, January 30, 2013

[Comp-neuro] 17th ICCNS conference: Call for Abstracts (February 28 contributed abstract submission deadline)

June 4 – 7, 2013
Boston University
677 Beacon Street
Boston, Massachusetts 02215 USA
Sponsored by the Boston University
Center for Adaptive Systems,
Center for Computational Neuroscience and Neural Technology (CompNet),
Center of Excellence for Learning in Education, Science, and Technology (CELEST)
with financial support from the National Science Foundation, pending final approval
This interdisciplinary conference is attended each year by approximately 300 people from 30 countries around the world. As in previous years, the conference will focus on solutions to the questions:
The conference is aimed at researchers and students of computational neuroscience, cognitive science, neural networks, neuromorphic engineering, and artificial intelligence. It includes invited lectures and contributed lectures and posters by experts on the biology and technology of how the brain and other intelligent systems adapt to a changing world. The conference is particularly interested in exploring how the brain and biologically-inspired algorithms and systems in engineering and technology can learn.  Single-track oral and poster sessions enable all presented work to be highly visible. Three-hour poster sessions with no conflicting events will be held on two of the conference days. Posters will be up all day, and can also be viewed during breaks in the talk schedule.
This year's conference will include, in addition to regular invited and contributed talks and posters, two workshops on the topics:
See the url above for the complete program of invited speakers.
Todd Braver (Washington University, St. Louis)
Flexible neural mechanisms of cognitive control: Influences on reward-based decision-making
Marisa Carrasco (New York University)
Effects of attention on early vision
Patrick Cavanagh (Harvard University and Université Paris Descartes)
Common functional architecture for spatial attention and perceived location
Robert Desimone [Plenary Speaker] (Massachusetts Institute of Technology)
Prefrontal-visual cortex interactions in attention
Asif Ghazanfar (Princeton University)
Evolving and developing communication through coupled oscillations
Stephen Grossberg (Boston University)
Behavioral economics and neuroeconomics: Cooperation, competition, preference, and decision-making
Joy Hirsch (Columbia University Medical Center)
Neural circuits for conflict resolution
Roberta Klatzky (Carnegie Mellon University)
Multi-modal interactions within and between senses
Kevin LaBar (Duke University)
Neural systems for fear generalization
Randi Martin (Rice University)
Memory retrieval and interference during language comprehension
Andrew Meltzoff (University of Washington)
How to build a baby with social cognition: Accelerating learning by generalizing across self and other
Javier Movellan (University of California, San Diego)
Optimal control approaches to the analysis and synthesis of social behavior
Mary Potter (Massachusetts Institute of Technology)
Recognizing briefly presented pictures: Feedforward processing?
Pieter Roelfsema (The Netherlands Institute for Neuroscience)
Neuronal mechanisms for perceptual organization
Daniel Salzman (Columbia University)
Cognitive signals in the amygdala
Daniel Schacter [Plenary Speaker] (Harvard University)
Constructive memory and imagining the future
Wolfram Schultz (University of Cambridge)
Neuronal reward and risk signals
Helen Tager-Flusberg (Boston University)
Identifying early neurobiological risk markers for autism spectrum disorder in the first year of life
Jan Theeuwes (Vrije Universiteit Amsterdam)
Prior history shapes selection
James Todd (Ohio State University)
The perception of 3D shape from texture
Leslie Ungerleider (National Institutes of Health)
Functional architecture for face processing in the primate brain
Jeremy Wolfe (Harvard Medical School and Brigham & Women's Hospital)
How selective and non-selective pathways contribute to visual search in scenes
Session Topics:
* vision                                                           * object recognition
* image understanding                               * neural circuit models       
* audition                                                       * neural system models                 
* speech and language                              * mathematics of neural systems 
* unsupervised learning                             * robotics       
* supervised learning                                  * hybrid systems (fuzzy, evolutionary, digital)
* reinforcement and emotion                     * neuromorphic VLSI
* sensory-motor control                               * industrial applications
* cognition, planning, and attention         * other
* spatial mapping and navigation                                    
Contributed abstracts must be received, in English, by February 28, 2013. Email notification of acceptance will be provided by March 15, 2013. 
Abstracts must not exceed one 8.5"x11" page in length, with 1" margins on top, bottom, and both sides in a single-column format with a font of 10 points or larger. The title, authors, affiliations, surface, and email addresses should begin each abstract. A separate cover letter should include the abstract title; name and contact information for corresponding and presenting authors; requested preference for oral or poster presentation; and a first and second choice from the topics above, including whether it is biological (B) or technological (T) work [Example: first choice: vision (T); second choice: neural system models (B)].
Contributed talks will be 15 minutes long. Posters will be displayed for a full day. Overhead and computer projector facilities will be available for talks. Copies of the accepted abstracts will be provided electronically to all registered conference participants and will be made publicly available via posting on the conference web site, in accordance with funding agency guidelines. No extended paper will be required.
A meeting registration fee must accompany each abstract. The fee will be refunded if the abstract is not accepted for presentation. Fees of accepted abstracts will be returned upon written request only until April 30, 2013.
Abstracts, cover letters, and completed registration forms with fee payment information should be submitted electronically using the phrase "17th ICCNS abstract submission" in the subject line.
Fax submissions of the abstract page will not be accepted. Fax or surface mail submissions of the registration form are acceptable (to Cynthia Bradford, using the contact information shown on the registration form below).
Student registrations must be accompanied by a letter of verification from a department chairperson or faculty/research advisor. Postdoctoral fellows and faculty members should register at the regular rate.
Seventeenth International Conference on Cognitive and Neural Systems
June 4 – 7, 2013
Boston University
677 Beacon Street
Boston, Massachusetts 02215 USA
Fax: +1 617 353 7755
City, State, Postal Code:______________________________________________
Phone and Fax:_____________________________________________________
The registration fee includes a conference reception and multiple daily coffee breaks.
(  ) $135 Conference (Regular)                
(  )   $85 Conference (Student)     
[   ] Enclosed is a check made payable to "Boston University"
Checks must be made payable in US dollars and issued by a US correspondent bank. Each registrant is responsible for any and all bank charges.
[   ] I wish to pay by credit card
      (MasterCard, Visa, or Discover Card only)
Name as it appears on the card:___________________________________________
Type of card: _____________________________ Expiration date:________________
Account number: _______________________________________________________

[Comp-neuro] Research Post available at Intelligent Systems Research Centre, University of Ulster, UK

Funding has been secured for a 6-month Research post to work on the development of a computational algorithm to test a novel brain inspired self-repairing concept developed at the University of Ulster in collaboration with the University of Liverpool. Specifically, the Research Associate will work on the development of a computer model of the self-repairing Spiking Neural Network (SNN) at the University of Ulster and will assist in how to translate the self-repairing capability to hardware. The Research Associate will be employed by Ulster for the duration of the project (6 months).


Applicants must have postgraduate research experience in a relevant area (e.g. Computer Science/Mathematics/Neuroscience), together with evidence of ability to develop computational biological models.


Deadline for applications is Feb 12th.

Further details can be found at the following URL:


Informal enquires are welcome and should contact Dr. Liam McDaid

School of Computing and Intelligent Systems

Faculty of Computing and Engineering

University of Ulster, Co. Derry

Northern Ireland BT48 7JL, UK

This email and any attachments are confidential and intended solely for the use of the addressee and may contain information which is covered by legal, professional or other privilege. If you have received this email in error please notify the system manager at and delete this email immediately. Any views or opinions expressed are solely those of the author and do not necessarily represent those of the University of Ulster. The University's computer systems may be monitored and communications carried out on them may be recorded to secure the effective operation of the system and for other lawful purposes. The University of Ulster does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of a separate attachment, the text of email is not intended to form a binding contract. Correspondence to and from the University may be subject to requests for disclosure by 3rd parties under relevant legislation. The University of Ulster was founded by Royal Charter in 1984 and is registered with company number RC000726 and VAT registered number GB672390524.The primary contact address for the University of Ulster in Northern Ireland is,Cromore Road, Coleraine, Co. Londonderry BT52 1SA

Tuesday, January 29, 2013

[Comp-neuro] Bernstein Network Computational Neuroscience: refilling the position of the Head of the National Coordination Site

The Bernstein Network Computational Neuroscience is refilling the position of the


Head of the National Coordination Site


The Bernstein Network is a German research network in the interdisciplinary field of Computational Neuroscience. It was initiated in 2004 by the Federal Ministry for Education and Research (BMBF) and connects over 200 research groups at more than 20 locations throughout Germany. The National Bernstein Coordination Site (BCOS) supports the network in all joint activities, represents the network nationally and internationally and is responsible for the joint press and public-relations work. Besides the position of its head announced here, BCOS consists of a scientific officer, a press and public relations officer and a project assistant.


Responsibilities of the BCOS head include:

  • Fostering the communication and scientific cooperation between the network partners and international contacts,
  • Organizational support for the yearly Bernstein Conference, planning and organization of further events and workshop,
  • Intensifying industry contacts
  • Support of young researchers and training
  • Development of long-term perspectives for the  Bernstein Network and lobbying
  • Contact to and service functions for the BMBF and the Project Agency, as well as contact to other funding agencies.   


The position comes with a broad spectrum of interesting tasks and offers numerous contacts and opportunities in a dynamic national and international research area.


Applicants should have a PhD or equivalent (preferentially in the neurosciences), own research experience and a good overview over the fields of Computational  Neuroscience and Neurotechnology. Experience in third-party funded projects and science management is expected. An excellent command of the German and English languages is required, as well as an integrative personality with pronounced social skills and a high degree of self-initiative. The position entails travelling within Germany as well as occasional international travelling.


We seek to fill the position as soon as possible. Salary level is up to TV-L E 15. Employment is currently limited until August 2015, prolongation on the basis of additional funding is being sought.


Further information on the Bernstein Network and its activities can be found at:  

Please direct your application (by February 15, 2013, one pdf file, < 5 MB) and any inquiries to: Dr. Simone Cardoso de Oliveira (


Dr. Simone Cardoso de Oliveira
Bernstein Network Computational Neuroscience
Head of the Bernstein Coordination Site (BCOS)
Albert Ludwigs University Freiburg
Hansastr. 9A
79104 Freiburg, Germany

phone: +49-761-203-9583
fax:    +49-761-203-9585

Twitter: NNCN_Germany
YouTube: Bernstein TV
Facebook: Bernstein Network Computational Neuroscience, Germany
LinkedIn: Bernstein Network Computational Neuroscience, Germany

[Comp-neuro] v5.5 of NeuroMorpho.Org

Version 5.5 of NeuroMorpho.Org was released on 15 January, 2013.

Twenty-six new data sets (872 reconstructions) have been added in this release.

The database now contains 8858 reconstructions from 108 labs.

Visit the What's New page ( for details on new data added in this release and other updates to the repository.

Visit the new About page ( for graphs of data trends and more.

Use the one-click option to view a random selection of neurons from the database (

As always, we are thankful to the data contributors and the NeuroMorpho.Org community for their continued support.

The NeuroMorpho.Org team

Ruchi Parekh, Ph.D.
NeuroMorpho.Org Project Lead
Center for Neural Informatics, Structures, and Plasticity
Krasnow Institute for Advanced Study
MS2A1, George Mason University
Fairfax, VA 22030 (USA)

[Genesis-sim-users] v5.5 of NeuroMorpho.Org

Version 5.5 of NeuroMorpho.Org was released on 15 January, 2013.

Twenty-six new data sets (872 reconstructions) have been added in this release.

The database now contains 8858 reconstructions from 108 labs.

Visit the What's New page ( for details on new data added in this release and other updates to the repository.

Visit the new About page ( for graphs of data trends and more.

Use the one-click option to view a random selection of neurons from the database (

As always, we are thankful to the data contributors and the NeuroMorpho.Org community for their continued support.

The NeuroMorpho.Org team

Ruchi Parekh, Ph.D.
NeuroMorpho.Org Project Lead
Center for Neural Informatics, Structures, and Plasticity
Krasnow Institute for Advanced Study
MS2A1, George Mason University
Fairfax, VA 22030 (USA)

Monday, January 28, 2013

[Comp-neuro] Postdoctoral postion in neurovascular coupling (imaging/electrophysiology)

A postdoctoral fellowship studying neurovascular coupling is available in the laboratory of Patrick Drew. We are looking for an independent, highly motivated scientist to use a combination of optical (two-photon microscopy and intrinsic imaging) and electrophysiological techniques to study neurovascular coupling in awake, behaving mice.

The successful applicant will have Ph.D. in neuroscience, biomedical engineering, or a related field, and at least one first author publication. The candidate should have excellent English communication skills, experience with in vivo electrophysiology and/or optical imaging techniques. Strong quantitative data analysis and signal processing skills are necessary. The position is for one year, with possibility extension up to two additional years contingent on funding and satisfactory performance.

Candidates should send a statement of research interests, a CV and three letters of reference to: Patrick Drew,

More information about the lab can be found here:

Applications will be reviewed upon receipt and will be accepted until the position is filled. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity and the diversity of its workforce.
Patrick J. Drew
Center for Neural Engineering
Dept. Engineering Science and Mechanics & Dept. Neurosurgery
The Pennsylvania State University
W-317 Millennium Science Complex
University Park, PA 16802
(814) 863-1473
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