# Caps Lock, what a useless key

1. [Ubuntu / gnome] You should be disable it do this with System->Preferences->Keyboard->Layouts->Options...->CapsLockkeybehavior
2. [MacosX] Open SystemPreferences, select the Keyboard pane. Within here, click the ModifierKeys… button at the bottom. To disable the Caps Lock key, pull down the associated menu and select NoAction.

# CRAAC: Compte rendu annuel d'activité des chercheurs du CNRS. Année 2010

2010-12-08 10:56:10

Compte rendu annuel d'activité des chercheurs du CNRS Année 2009 - 2010

# ignoring a folder in SVN

• simply issue

svn propset svn:ignore '*' data/


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.

# Instinct Paradise :-journée IMERA du 9 nov 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:

# 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 

# installing python and its components

• Python is often pre-installed on your system or easy to download. More difficult is to get the essential packages (numpy, scipy, matplotlib, ipython) and their dependencies installed. Here, I list some of the possibilities.

# nous

• ﻿http://en.wikipedia.org/wiki/Nous
• 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).

# Journée de l'IFR 131 -Sciences du Cerveau et de la Cognition

Aujourd'hui avait lieu la journée de l'IFR, pendant laquelle nous sommes intervenu avec F._X. Alario et A. Montagnini sur le thème de la variabilité comportementale.

# 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)

# Terminal.app shortcuts

• To make Ctrl← and Ctrl→  useful again, that is going a word forward or backward like they usually do on Linux, you must make Terminal.app 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.


• install a package

sudo installer -pkg <chemin d’accès au paquet> -target /


# getting the PID from matlab

• I need the pid to know if one of the many simulations I run are still running. There's no native solution in matlab to my knowledge.

# running embarassingly parallel simulations on a multicore machine using bash loops

• I need to run a single-processor experiment on some parameters, say N times

# 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, ...)

# Pinna illusion

• 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).


# compiling OpenCV on MacOSX 10.6

## using macports

• it works now with macports:

sudo port install -u opencv +python26 +tbb


# latex within moinmoin

• installation d'après http://johannes.sipsolutions.net/Projects/new-moinmoin-latex

• pour s'adapter à ma distribution pdflatex, j'ai changé

1 # last arg must have %s in it!
2 latex_args = ("--interaction=nonstopmode -output-format dvi", "%s.tex")


dans le parser sudoopen-e~/WebSites/moin/data/plugin/parser/latex.py)

# NeuroCompMarseille 2010 Workshop

Computational Neuroscience: From Representations to Behavior

Second NeuroComp Marseille Workshop

Date
27-28 May 2010

# 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.

# replacing text in files

## using sed

• The UNIX command sed is useful to find and replace text in single or multiple files. This page lists some common commands in using sed to improve editing code.

# using grin

• I just discovered grin, "grep my way"

# 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 whichssh to locate the binary.

# quelques blogs français de science

Wikio permet de rechercher tout blog / article de blog relié par ex aux Neurosciences.

# 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.

# contributing to the python community

(or "would be hard to give as much as I took :-)" )

# which or that?

That usually introduces essential information in what is called a "restrictive clause." Which introduces extra information in a "nonrestrictive clause."


# CRAAC: Compte rendu annuel d'activité des chercheurs du CNRS. Année 2008 - 2009

 Compte rendu annuel d'activité des chercheurs du CNRS Année 2008 - 2009

# some unix tips

• find / -nouser te donneras tous les fichiers dont le nom du propriétaire est inexistant de la table /etc/passwd

# MoinMoin: howto install a new theme

• locally

scp Downloads/moniker18_2.1.1.zip  perrinet@195.221.164.4:/var/www/moin/perrinet/data/plugin/theme/tmp

.. TEASER_END

• 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
unzip moniker18_2.1.1.zip
cd moniker18_2.1.1
cp -r moniker /usr/share/moin/htdocs/
cp moniker18.py ../../
chgrp -R $GROUP$INSTANCE
chgrp -R \$GROUP ../../moniker18.py
vim ../../../../../../perrinet.py # set moniker18 as default


# floating point magic

• bug or feature?

python

>>> 1-.9-.1
-2.7755575615628914e-17

.. TEASER_END

• 1= 0

• Q: How many Pentium designers does it take to change a light bulb? A: 1.99904274017, but that's close enough for non-technical people.

• http://docs.sun.com/source/806-3568/ncg_goldberg.html

# Tips on Filesystems, security and al on mac os x

• mount with AFP sharepoints from the command line (thanks to this hint) :

# mount_afp [-i] [-o options] afp_url node
mkdir /Volumes/truc
umount /Volumes/truc
rmdir /Volumes/truc


# 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).

# setting graphics' path

\includegraphics[width=\textwidth]{folder2_relative/picture.png}%


# some LaTeX tips: drafts, links, margins, pdflatex

More \LaTeX tips...

# Installation TeX

Some useful bits of \LaTeX code accumulated over the years...

# 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 .

# keyboard

## Touches spéciales (unix) sur clavier Mac francais

Merci a http://busy.lab.free.fr/mac/ !

 backslash \ shift + option + / pipe, or | shift + option + L tidle ~ 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 + )

# 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.

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

Warning

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.

# 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.