Merge branch 'master' of git.debian.org:/git/pkg-exppsy/neurodebian

* 'master' of git.debian.org:/git/pkg-exppsy/neurodebian:
  FIX: oops - I did it again
  Added [ua] mirror
  Live image page: installation instructions, version history, added screenshot; derivatives page: added NeuroDebian packages included (2nd try)
  Live image page: installation instructions, version history, added screenshot; derivatives page: added NeuroDebian packages included
  oopsy -- fixing what should have not been committed
  Added a basic icon for derivatives page

diff --git a/Makefile b/Makefile
index 4b9e35a7c432e465bdc0be57ec29b89b60395f49..34adc54d81ca074b34ff39f086714db3522165cf 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -10,7 +10,7 @@ pics:
 
 
 html: pics source
-       rsync -rvlhp sphinx/ build/src
+       rsync -rvlhpt sphinx/ build/src
        cd artwork;     cp button_w200.png logo_tuned/fmri_w200.png ../build/src/_static; cd ..
        cp 3rd/jquery.livetwitter/jquery.livetwitter.min.js build/src/_static
        cd build/src && $(MAKE) html BUILDDIR=$(CURDIR)/build 2>&1

diff --git a/artwork/.gitignore b/artwork/.gitignore
index 70b71e2c60c8cba8230c7bd11f94092be58f6e94..320616afd542465003f399f2fc0fa74262157a3c 100644 (file)
--- a/artwork/.gitignore
+++ b/artwork/.gitignore
@@ -12,3 +12,4 @@ openlogo-vsop.pdf
 banner.pdf
 qrcode_sticker.pdf
 qrcode_sticker.png
+derivatives.png

diff --git a/artwork/derivatives.svg b/artwork/derivatives.svg
new file mode 100644 (file)
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--- /dev/null
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diff --git a/neurodebian.cfg b/neurodebian.cfg
index 81ffe25ca6c2cad1367316670b329898a8517741..1703f898f9bbe9a1222e871d1cda10b8fe0e3f86 100644 (file)
--- a/neurodebian.cfg
+++ b/neurodebian.cfg
@@ -67,6 +67,7 @@ au = http://mirror.aarnet.edu.au/pub/neurodebian
 de = http://apsy.gse.uni-magdeburg.de/debian
 gr = http://neurobot.bio.auth.gr/neurodebian
 jp = http://neuroimaging.sakura.ne.jp/neurodebian
+ua = http://www.neuro.webdisk.com.ua
 us-ca = http://neurodeb.pirsquared.org
 us-nh = http://neuro.debian.net/debian
 us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
@@ -76,6 +77,7 @@ au = Australia (AARNET)
 de = Germany (University of Magdeburg)
 gr = Greece (Aristotle University of Thessaloniki)
 jp = Japan (Kiyotaka Nemoto)
+ua = Ukraine (Iaroslav Iurchenko)
 us-ca = USA-CA (Paul Ivanov, California)
 us-nh = USA-NH (Dartmouth College)
 us-tn = USA-TN (Vanderbilt)

diff --git a/sandbox/2012-02-08_comp_neurosci_ubuntu_live_usb.rst b/sandbox/2012-02-08_comp_neurosci_ubuntu_live_usb.rst
index 1a97560b0f7495fea6c6f74843e133f1b1960b20..e7c6c7b3dd33efe20589637c8a04633e04961d0e 100644 (file)
--- a/sandbox/2012-02-08_comp_neurosci_ubuntu_live_usb.rst
+++ b/sandbox/2012-02-08_comp_neurosci_ubuntu_live_usb.rst
@@ -6,6 +6,12 @@
 A Live Ubuntu/NeuroDebian USB Stick for Computational Neuroscience
 ====================================================================
 
+ .. image:: screenshot-genesis-neuron-xpp.png
+       :width: 150px
+       :alt: View of the desktop running GENESIS, Neuron and XPPAUT
+       :align: right
+       :target: screenshot-genesis-neuron-xpp.png
+
 I prepared an `Ubuntu 11.04`_/NeuroDebian_ live image with computational neuroscience tools for mainly use in USB sticks. This live image will let you run a full `Live Ubuntu Linux`_ system **without installing anything on your hard drives**, and it includes `persistent storage`_ that **maintains new files and packages across reboots**. The system is bundled with several computational neuroscience tools like GENESIS_, NEURON_ and XPPAUT_. It is made to fit in USB sticks of size >1GB. To use it, you will have to restart your PC with the USB stick inserted. After you turn on your computer, you will possibly also need to bring up your boot menu and choose to boot from the USB stick (most likely by pressing F10 or F12). 
 
 .. _`Ubuntu 11.04`: http://help.ubuntu.com/11.04/ubuntu-help/index.html
@@ -34,6 +40,17 @@ As a first precaution, the USB stick should be routinely backed up. You can also
 
 *Disclaimer: I take no responsibility over lost data whatsoever. By using this image, you assume all responsibility of your data.*
 
+Installing the ISO image onto a USB flash drive:
+------------------------------------------------
+Download the ISO image from the `NeuroDebian Derivatives page`_. Use a
+utility like UNetBootin_ to install the ISO image on your USB
+drive. Keep the persistent space setting at zero, as otherwise it
+will overwrite our image. *Simply extracting the ISO would not work as
+the media needs to be set to bootable.*
+
+.. _UNetBootin: http://unetbootin.sourceforge.net/
+.. _`NeuroDebian Derivatives page`: http://neuro.debian.net/derivatives.html
+
 Copying files to your hard drives:
 -----------------------------------
 Open the file browser by clicking on the home icon in the left sidebar on the Desktop. In the file browser window, you should be able to see your hard drives on the left sidebar. When you click on them, they will be "mounted" (i.e., become visible) and show up as directories under /media. Then, you can copy files back and forth.
@@ -77,7 +94,9 @@ Which should give you root access. And then run the disk check:
 
  # e2fsck -p /cdrom/casper-rw
 
-Press "y" and enter for the questions that it asks. Should not ask more than 10-20 of them. After this you should be able to reboot back into the Live Ubuntu.
+Press "y" and enter for the questions that it asks. Should not ask
+more than 10-20 of them. After this you should be able to reboot back
+into the Live Ubuntu.
 
 Installing Ubuntu completely on your hard drive for dual booting
 ----------------------------------------------------------------
@@ -85,11 +104,24 @@ Click on the "Install Ubuntu 11.04" link on the Desktop and follow the instructi
 
 Other troubleshooting:
 ----------------------
-This Live USB Stick is completely based on a Ubuntu 11.04 Live CD distribution. Please refer to their thorough documentation for further issues: https://help.ubuntu.com/community/LiveCD
+This Live USB Stick is completely based on a Ubuntu 11.04 Live CD
+distribution. Please refer to their thorough documentation for further
+issues: https://help.ubuntu.com/community/LiveCD
+
+.. admonition:: Revision History
+
+ *v2*, by CG on 2012-03-06
+  Included the NeuroDebian repository, and installed
+  XPPAUT and python-brian (with all python dependencies for
+  computational modeling) packages.
+
+ *v1*, by CG on 2012-01-31
+  Initial version with manual installations of GENESIS, NEURON and
+  XPPAUT onto Ubuntu 11.04 Live CD.  
 
 .. admonition:: Created by...
 
-  | *v1* created on 2012-01-31 for use at the `Emory University <http://www.emory.edu>`_ BIO450/IBS534 Computational Neuroscience Course by Cengiz Gunay <cgunay AT emory.edu>, <cengique AT users.sf.net>
+  | Created for use at the `Emory University <http://www.emory.edu>`_ BIO450/IBS534 Computational Neuroscience Course by Cengiz Gunay <cgunay AT emory.edu>, <cengique AT users.sf.net>
 
  .. image:: CC_by_3.0_88x31.png
        :alt: Creative Commons License

diff --git a/sandbox/screenshot-genesis-neuron-xpp.png b/sandbox/screenshot-genesis-neuron-xpp.png
new file mode 100755 (executable)
index 0000000..046b710
Binary files /dev/null and b/sandbox/screenshot-genesis-neuron-xpp.png differ

diff --git a/sphinx/_static/derivatives.png b/sphinx/_static/derivatives.png
new file mode 100644 (file)
index 0000000..1e039e8
Binary files /dev/null and b/sphinx/_static/derivatives.png differ

diff --git a/sphinx/derivatives.rst b/sphinx/derivatives.rst
index b80cbaf35c0f835efbe9c1b3546830473e1bf000..a076a72f0e9f904e6581494e9f03910eb0177858 100644 (file)
--- a/sphinx/derivatives.rst
+++ b/sphinx/derivatives.rst
@@ -44,7 +44,7 @@ USB Stick for Computational Neuroscience by Cengiz Günay
 |                           | - Based on Ubuntu_ 11.04                              |
 +---------------------------+-------------------------------------------------------+
 |**Pre-installed Software** | NeuroDebian                                           |
-|                           |  TBA                                                  |
+|                           |  XPPAUT_ 6.11b, python-brian_                               |
 |                           | Custom:                                               |
 |                           |  Genesis_ 2.3, Neuron_ 7.2, XPPAUT_ 6.10              |
 +---------------------------+-------------------------------------------------------+

diff --git a/sphinx/index.rst b/sphinx/index.rst
index 591b7e4007ac70471eb920367f6fd874bf8d0e25..a869efadb5beace450fac821b15830f8bfabbb3f 100644 (file)
--- a/sphinx/index.rst
+++ b/sphinx/index.rst
@@ -36,6 +36,7 @@ please `report <#contacts>`_ them.
  <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
  <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
  <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
+ <a href="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
  <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
  </p>
 
@@ -221,6 +222,7 @@ Thanks to the following institutions and individuals for hosting a mirror:
 * `Australia's research and education network (AARNET)
   <http://www.aarnet.edu.au>`_ *[au]*
 * Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
+* Iaroslav Iurchenko *[ua]*
 
 If your are interested in mirroring the repository, please see the :ref:`faq`.