Ermentrout : "Double or Nothing: Phosphenes and the periodic driving of cortex"


    Bard Ermentrout
    Department of Mathematics
    University of Pittsburgh
    Wednesday 9 March 2011, 16:00
    Seminar Room, Wellcome Trust Centre for Neuroimaging (FIL)
    12 Queen Square, London, WC1N 3AR
    Double or Nothing: Phosphenes and the periodic driving of cortex
    In this talk, I examine two different types of phosphenes - patterns in the visual systems evoked from within it. I first study contour phosphenes in which direct stimulation of the eyeball coupled with a moving bar in the visual field produces slowly propagating waves. The mechanism appears to be due to period doubling which produces an intrinsic bistability. Using averaging, I analyze the dynamics of a one-dimensional analog. In the second part of the talk, I study flicker-induced hallucinations in which diffuse stroboscopic light is capable of  evoking spatial patterns in the visual field. I use Floquet theory and symmetric bifurcation theory to explain experiments that indicate different patterns are seen with different temporal frequencies.

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ubuntu : starting sshd at boot

  • ssh server installed but not starting at boot (I certainly messed up something):

    $ ls -l /etc/init.d/*ssh*
    -rwxr-xr-x 1 root root 3704 2010-09-14 19:20 /etc/init.d/ssh
    $ ls -l /etc/rc2.d/*ssh*
    ls: cannot access /etc/rc2.d/*ssh*: No such file or directory
    $ ls -l /etc/rc1.d/*ssh*

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Caps Lock, what a useless key

  1. [Ubuntu / gnome] You should be disable it do this with System->Preferences->Keyboard->Layouts-> Options...->CapsLock key behavior

  2. [MacosX] Open System Preferences, select the Keyboard pane. Within here, click the Modifier Keys… button at the bottom. To disable the Caps Lock key, pull down the associated menu and select No Action.

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Password-less logins with OpenSSH

Because OpenSSH allows you to run commands on remote systems, showing you the results directly, as well as just logging in to systems it's ideal for automating common tasks with shellscripts and cronjobs. One thing that you probably won't want is to do though is store the remote system's password in the script. Instead you'll want to setup SSH so that you can login securely without having to give a password.

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Instinct Paradise :-journée IMERA du 9 nov 2010

journée IMERA du 9/11/2010

Mon projet scientifique s'intéresse aux mécanismes computationnels qui sous-tendent la cognition. C'est-à-dire que l'on sait que l'on sait où se produisent ces mécanismes définissant la système nerveux central en un réseau de neurones connectés par des synapses et qu'ils sont supportés par des signaux électro-chimiques entre ces noeuds, mais on ne connaît pas encore totalement comment l'information qui semble être portée ces signaux peut être interprété. Ce "Graal" est la découverte du "code neural" c'est-à-dire du langage qui est utilisé dans notre cerveau. On ne sait si cette découverte est possible: peut-il exister une connaissance globale du cerveau comme on peut deviner la trajectoire d'une planète avec les lois de Newton? Peut-etre le cerveau lui-même n'est pas assez complexe, même mis en réseau avec tous les neuro-scientifiques du monde entier, pour se laisser deviner... Mais il y a de nombreuses perspectives à le découvrir progressivement:

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rsync to an alternate ssh port

  • Q: sometimes you try to copy files using rsync but the server uses an alternate port than the usual 22...

  • A: `` rsync -av -e 'ssh -p 2222' HOST:~/folder/* dest ``



  • Nous (pronounced /ˈnuːs/, Greek: νοῦς or νόος) is a philosophical term for mind or intellect. Outside of a philosophical context, it is used, in coloquial English, to denote "common sense," with a different pronunciation (/naʊs/), and sometimes a different spelling (nouse or nowse).

A neurocentric approach to Bayesian inference

  • one-page paper arguing that Friston's free-energy view may not be complete. Some points made are

    1. the inversion operated assumes a generative model

    2. the use of surprise is defined using a frequentist approach not informational

      • one idea : from the frequentist measure one one can derive a conditional probability (a Xhi-2 distribution) of the probability. Not very far to the idea of Sahani & Dayan of a double probabilistic distribution

    3. explore surprise or avoid it: Fiorillo makes here a confusion of time scales. On the long term (learning) one tends to avoid surprise, on the short term (coding) this implies one jumps one surprise.

    4. points to his PLoS one paper: Fiorillo, C. D. Towards a general theory of neural computation based on prediction by single neurons. PLoS ONE 3, e3298 (2008)

Read more… shortcuts

  • from

    To make Ctrl← and Ctrl→  useful again, that is going a word forward or backward like they usually do on Linux, you must make send the right string to the shell. In the preferences, go to the Settings tab and select your default profile. Go to Keyboard and set control cursor left and control cursor right to send string \033b and \033f respectively.
    While your're at it, you can also fix Home (\033[H), End (\033[F), Page Up (\033[5~) and Page Down (\033[6~) so that they send those keys to the shell instead of scrolling the buffer.

distributed computing

  • guess you have a bunch (4000) of embarrassingly parallel tasks (one hour each) and access to about 40 CPUs through SSH. All tasks would run easily on each node, and they all share some network drive (NFS). Would be nice to run everything from just one place (script, command-line, web interface, ...)

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Pinna illusion

  • from :

    Pinna illusion is the first visual illusion showing a rotating motion effect. In Figure 1  the squares, delineated by two white and two black edges each, are grouped by proximity in two concentric rings. All the squares have the same width, length, and orientation in relation to the center of their circular arrangements. The two rings differ only in the relative position of their narrow black and white edges forming the vertexes. More precisely, the two rings show reversal of the vertex orientation and, consequently, opposite inclination of the virtual or implicit diagonal orientation polarity obtained by joining the two vertexes where black and white lines meet (Pinna, 1990; Pinna & Brelstaff, 2000).

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Haïm Cohen : Tu Ne Laisseras Point Pleurer

  • Présentation de l'éditeur (source: amazon)

    • Où puiser l'espoir d'un monde plus humain ? En comprenant la dimension humaine des pleurs de nos bébés et en y répondant encore et encore. A partir d'arguments psychologiques et neurobiologiques, Haïm Cohen nous expose son utopie susceptible d'élever la conscience morale de nos enfants ainsi immunisés contre l'extrême violence. Manuel d'humanisme autant que de réflexion portée sur notre société, ce livre s'adresse à tous les parents soucieux du bon développement psycho-affectif de leur enfant, mais aussi à tous les lecteurs intéressés par les progrès des neurosciences.

    • Biographie de l'auteur : Haïm Cohen est pédiatre à Paris.

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securing the server

  • SSH (Secure Shell) is installed on most systems (here GnuLinuxUbuntu and MacOsX) so don't panic about compilations (try Putty on Windows). Try a simple ssh -V to check version or which ssh to locate the binary.

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The original eve

  • one common statement in popular science when speaking about evolution is that we all derive from a common ancestor, the "original eve". while a posteriori, it is true that mitochodrondrial DNA allows to trace back common ancestors in our heredity, it is certainly overstated. When thinking evolution, our focus is to look back from the present to our origins, but a the time of these "few" original eves, many different eves coexisted and acted -as parts of the whole population- in the evolution.

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MoinMoin: howto install a new theme

  • locally

    scp Downloads/  perrinet@
  • on the server

    cd /var/www/moin/perrinet/data/plugin/theme/
    export USER=www-data
    export GROUP=www-data
    export INSTANCE=/usr/share/moin/htdocs/moniker
    cd moniker18_2.1.1
    cat read\ me\ on\ installing.txt
    cp -r moniker /usr/share/moin/htdocs/
    cp ../../
    chgrp -R $GROUP $INSTANCE
    chgrp -R $GROUP ../../
    vim ../../../../../../ # set moniker18 as default

Creating Proceedings (almost) automatically using python and latex

In order to produce proceedings for the NeuroComp08 that we organized, I used a combination of LaTeX and Python to generate a PDF from our preprint server based on ConfMaster. This was due to the lack of an appropriate tool for this system and the need to be flexible to any change made in last minute by the authors. I used the following steps (these are summarized in the included Makefile file at the bottom that allowed to rebuild everything when any small change in these steps were done).

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duplicate files

You may find yourself overwhelmed by files and in the need to keep the filesystem organized. If deleting is the best option, you may consider these 2 options:

Impact Factor

Most researchers nowadays are judged based on their publication list and ---as a shortcut--- quantifically rated by their cumulative Impact Factor. How efficient is this method?

  • This paper studies the assumptions underlying the journals' impact factor and the open access initiative:

    • M. Taylor, P. Perakakis, Varvara Trachana. The siege of science , URL . Ethics in Science and Environmental Politics, 8(1):17--40, 2008 .


Touches spéciales (unix) sur clavier Mac francais

Merci a !



shift + option + /

pipe, or


shift + option + L



option + N

simple quote


4 key, that's to say a regular ' on any keyboard I guess.

opening brace


option + (

closing brace


option + )

opening square bracket


shift + option + (

closing square bracket


shift + option + )

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Deliverable M9-3: Workshop for definition of a detailed version of the V1 hypercolumn model

The INCM was holding a workshop on the V1 hypercolumn model on the 22nd and 23rd of October 2007. The purpose of the workshop was to promote the coordination of modeling efforts within the consortium and in particular to organize collaboration in WP9T2 and associated work-packages. It is labeled as deliverable M9-3: "Workshop for definition of a detailed version of the V1 hyper-column model" for WP9-2 (workpackage 9 task 2), but is also linked by its subject to WP5. In contrast to the previous meeting, we started with brief presentations of the results from each group to expose the different efficient aspects of each model. This allowed us in the second half of the workshop to converge to some main issues and prioritize the neural features that are the most important for the efficiency of V1. As for the format, we proposed that PhD students and post-docs should have the opportunity to present this work to give them experience and reduce the burden on busy chiefs. We felt it was important to involve as many in this workshop as possible as we approach a crucial stage in integrating the different models.

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Post-doctoral Position in Computational Neuroscience: "Functional, Large-scale Models of Visual Motion Perception"


The position has been filled

We are currently inviting applications for a postdoctoral position in computational neuroscience to study functional, large-scale models of visual motion perception. The post is for up to 3 years in the DyVA team at the INCM (CNRS) in Marseille, France and will be funded within the european FACETS consortium.

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V1 hypercolumn Coordination Meeting, 20th - 21st Nov 2006

Subject: Coordination meeting of the WP9T2 and WP5T3 tasks.

  • The goal of the meeting was to prepare the next deliverable D25 ("model of an hyper-column") but also to join our efforts in modeling. In particular, important decisions were made toward finding canonical parameters (structure, neural parameters) of all systems being delivered in WP5T3 and WP9T2 but also concerning the definition of the common benchmark that will de deployed to the different implementations in the different partners. From this benchmark (benchmark zero), we should be able to validate different solutions to pinpoint their strengths and weaknesses.

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CRAAC 2005


Récapitulatif de votre saisie : ce document sera soumis au visa de votre directeur

Compte rendu annuel d'activité des chercheurs du CNRS Année 2004 - 2005

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