From: Cengiz Günay Date: Mon, 20 Feb 2012 01:32:38 +0000 (-0500) Subject: Merge remote branch 'origin' X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=418ad95a1bde551ab6cf8229f24615dc5ab5c24d;hp=e3fc84d088bdac28c79356c270ee3e0b2713514b;p=neurodebian.git Merge remote branch 'origin' --- diff --git a/future/blends/eeglab b/future/blends/eeglab index 55a9560..58f737d 100644 --- a/future/blends/eeglab +++ b/future/blends/eeglab @@ -1,6 +1,7 @@ Source: eeglab Tasks: debian-science/neuroscience-cognitive, - debian-med/imaging + debian-science/electrophysiology, + debian-med/imaging Homepage: http://sccn.ucsd.edu/eeglab Responsible: NeuroDebian Team Language: C, Matlab/Octave @@ -8,6 +9,7 @@ Version: 9 Author: Arnaud Delorme , Scott Makeig License: GPL-2+ WNPP: 605739 +Pkg-URL: http://neuro.debian.net Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics Published-Authors: Delorme A and Makeig S Published-In: Journal of Neuroscience Methods 134:9-21 diff --git a/neurodebian.cfg b/neurodebian.cfg index 5efe97e..ece9fea 100644 --- a/neurodebian.cfg +++ b/neurodebian.cfg @@ -22,7 +22,7 @@ select names = libnifti2 odin mitools afni-atlases python-pyssdh python-networkx r-cran-glmnet python-rpy2 python-nibabel-snapshot python-sklearn python-scikits-learn python-mdp python-mlpy python-openpyxl libgdf-dev matlab-support svgtune rorden-mri-tutorial caret-data python-joblib python-sphinx fail2ban - python-pandas neurodebian numdiff nuitka + python-pandas neurodebian numdiff nuitka pytables # Information about prospective packages to be imported from taskfiles prospective = @@ -42,6 +42,7 @@ prospective = # to be added as an alias as well cctools = coop-computing-tools mni-icbm152-nlin-2009 = mni-icbm152-nlin-2009a mni-icbm152-nlin-2009b mni-icbm152-nlin-2009c +eeglab = matlab-eeglab11 eeglab11-sampledata fsl = fsl fsl-doc fsl-atlases fsl-possum-data fsl-first-data fsl-feeds fsl-mni152-templates fslview = fslview fslview-doc python-mvpa = python-mvpa python-mvpa2 @@ -58,6 +59,7 @@ pysurfer = python-surfer pyxnat = python-pyxnat openwalnut = openwalnut-qt4 neurodebian = neurodebian-dev neurodebian-desktop neurodebian-keyring neurodebian-popularity-contest neurodebian-guest-additions +pytables = python-tables [mirrors] au = http://mirror.aarnet.edu.au/pub/neurodebian diff --git a/sphinx/derivatives.rst b/sphinx/derivatives.rst new file mode 100644 index 0000000..588dc76 --- /dev/null +++ b/sphinx/derivatives.rst @@ -0,0 +1,78 @@ +.. -*- mode: rst; fill-column: 78 -*- +.. ex: set sts=4 ts=4 sw=4 et tw=79: + +.. _chap_derivatives: + +************************* +NeuroDebian "Derivatives" +************************* + +NeuroDebian_ is not a *Linux distribution* in a traditional sense because we +work within Debian_ project thus not providing our custom installer etc. But +we are a Linux-distribution providing a repository of up-to-date builds and +maintaining a :ref:`chap_vm` deployment of Debian. Because of the openness +and modularity of Debian other enthusiasts develop customized derivative +solutions based to address a particular demand. + +This page presents such *derivative* projects which are tuned for particular +domains of application in neuroscience and rely on NeuroDebian_ as the origin +for necessary tools. + +.. note:: + + These projects are not maintained by NeuroDebian_ team. Please direct all + you support inquiries to respective authors/maintainers. + + +Live CD/USB Media +================= + +USB Stick for Computational Neuroscience by Cengiz Günay +-------------------------------------------------------- + ++---------------------------+-------------------------------------------------------+ +|**Author** |Cengiz Günay | ++---------------------------+-------------------------------------------------------+ +|**Homepage** | N/A | ++---------------------------+-------------------------------------------------------+ +|**Purpose** | Computational neuroscience tools for course-work | ++---------------------------+-------------------------------------------------------+ +|**Features** | - Persistent Storage | +| | - XXX | ++---------------------------+-------------------------------------------------------+ +|**Pre-installed Software** | NeuroDebian | +| | Brian (XXX?), XXX | +| | Custom: | +| | Genesis, Neuron, XPPAUT | ++---------------------------+-------------------------------------------------------+ +|**Download** | http://neuro.debian.net/debian/live/3rd/XXX.iso [2GB] | ++---------------------------+-------------------------------------------------------+ +|**References** | XXX point to the blog entry whenever is ready | ++---------------------------+-------------------------------------------------------+ + + +Lin4Neuro +--------- + + +Virtual Appliances +================== + +* XNAT +* MIPAV + + +Cloud Environments +================== + +* NITRC? + + +Cloud Images +============ + +* UK Grant project +* INCF Cloud App? + + +.. include:: link_names.txt diff --git a/sphinx/index.rst b/sphinx/index.rst index ab7f745..052c687 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -97,7 +97,7 @@ the terminal you can use :command:`apt-get`:: Popularity Contest ------------------ -We would strongly encourage you to participate in the `popularity +We encourage you to participate in the `popularity contest `_ (popcon), which anonymously collects the list of packages you installed/use on your system. Collecting such statistics is of particular importance for research @@ -230,6 +230,17 @@ If your are interested in mirroring the repository, please see the :ref:`faq`. Publications ============ +Halchenko, Y.O. & Hanke, M. (2012). `Environments for efficient +contemporary research in neuroimaging: PyMVPA and NeuroDebian +<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_. +*Talk given at the University of Pennsylvania School of Medicine*, +Philadelphia, PA, USA. + +Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke: +NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_. +*Talk given at the Max-Planck-Institute for Human Cognitive and Brain +Sciences*, Leipzig, Germany. + Hanke, M. (2011). `More than batteries included: NeuroDebian <_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_. *Talk given at the Python in Neuroscience satellite of EuroScipy 2011*, diff --git a/sphinx/proj_matlab.rst b/sphinx/proj_matlab.rst index a799483..56d3ac1 100644 --- a/sphinx/proj_matlab.rst +++ b/sphinx/proj_matlab.rst @@ -41,13 +41,15 @@ with Octave, as well as developing patches to achieve such compatibility. Status ------ -A :ref:`Matlab-support package ` draft is ready, available -from NeuroDebian, and has been uploaded to `Debian NEW queue -`_ . +A :ref:`Matlab-support package ` is available starting from +Debian 7.0 (wheezy) and Ubunty 11.10 (oneiric). Backports for older releases can +be obtained from NeuroDebian. -Packaging of individual Matlab-based software has started. This includes -:ref:`SPM ` and :ref:`Fieldtrip ` (see -references_ for more packages). Expanding the coverage is planned. +Packaging of individual Matlab-based software has started. An +:ref:`SPM ` package is ready, and a preliminary package of +:ref:`EEGLAB ` is available from NeuroDebian. +An upcoming :ref:`Fieldtrip ` package is work-in-progress (see +references_ for more packages). Further expansion of the coverage is planned. .. todo:: Integrating Matlab-based software @@ -57,17 +59,6 @@ references_ for more packages). Expanding the coverage is planned. complement :ref:`octave-psychtoolbox-3 `. * Create :ref:`matlab-biosig ` to complement :ref:`octave-biosig `. - * Package `EEGLAB `_. - -.. note:: Done: - - * Adapt the packaging of `dynare `_ - in Debian to use the new support package. Once this is done and reviewed by - its maintainers the support package can be submitted for inclusion into - Debian proper. - * Upload :ref:`libgdf ` (including :ref:`matlab-gdf - `) to Debian proper as soon as :ref:`matlab-support - ` is accepted References ---------- diff --git a/tools/nd_apachelogs2subscriptionstats b/tools/nd_apachelogs2subscriptionstats index 6ecc7c7..b39df16 100755 --- a/tools/nd_apachelogs2subscriptionstats +++ b/tools/nd_apachelogs2subscriptionstats @@ -27,9 +27,9 @@ dt = [('ip', '|S16'), def make_figure(data): fig = pl.figure(figsize=(14,3)) ax = fig.add_subplot(121) - plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Debian')], title="Debian", ymax=10) + plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Debian')], title="Debian", ymax=11) ax = fig.add_subplot(122) - plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Ubuntu')], title="Ubuntu", ymax=10) + plot_datehist(ax, data, 10, [code for code in cfg.options('release codenames') if cfg.get('release codenames', code).count('Ubuntu')], title="Ubuntu", ymax=11) fig.autofmt_xdate() return fig