draft version of comp neurosci live usb stick blog page w/o download links

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+:date: 2012-02-08 19:02:00
+:tags: neuroscience, computational neuroscience, ubuntu, software, live cd, usb disk, linux distribution
+
+.. _chap_comp_neurosci_ubuntu_live_usb:
+
+A Live Ubuntu USB Stick for Computational Neuroscience
+=================================================================
+
+I recently prepared a Computational Neuroscience `Ubuntu 11.04`_ USB Stick image, which NeuroDebian_ kindly offered to host. This USB stick 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
+.. _GENESIS: http://www.genesis-sim.org/GENESIS/
+.. _NEURON: http://neuron.duke.edu/
+.. _XPPAUT: http://www.math.pitt.edu/~bard/xpp/xpp.html
+.. _NeuroDebian: http://neuro.debian.net
+.. _`Live Ubuntu Linux`: http://help.ubuntu.com/community/LiveCd
+.. _`persistent storage`: http://help.ubuntu.com/community/LiveCD/Persistence
+
+***************************************************************************
+WARNING   WARNING   WARNING   WARNING   WARNING   WARNING   WARNING   
+***************************************************************************
+As a fully running Linux system, this USB stick is not perfect. It will `get corrupted over time`_ and special care needs to be taken to maintain its health. As a precaution backups of it should be made routinely. You can also copy your files over to your hard drive. For performance issues, it is possible to transfer the persistent storage to your hard drive. See below for details.
+
+.. _`get corrupted over time`: http://bugs.launchpad.net/ubuntu/+source/upstart/+bug/125702
+
+FOLLOW THESE RULES:
+
+1. NEVER YANK OUT THE USB STICK WHILE UBUNTU IS RUNNING. PERFORM PROPER "SHUTDOWN" FIRST.
+
+2. REGULARLY BACKUP DATA FROM USB STICK ONTO HARD DRIVE
+
+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.
+
+Backing up the persistent storage that holds your files:
+--------------------------------------------------------
+Do this routinely to save your new files on the USB stick:
+
+1. While running Windows, insert USB stick 
+
+2. Copy file "casper-rw" on your Desktop, preferably with a date
+
+To restore it, copy it back on the USB and make sure it's named "casper-rw"
+
+Transferring the persistent storage to your Windows hard drive:
+---------------------------------------------------------------
+
+1. While running Windows, insert USB stick 
+
+2. Copy file "casper-rw" to the root of one of your hard disks (e.g. C:\\casper-rw). Ubuntu will find it and use it from there. Keep on making backups of it as it can still get corrupted over time.
+
+3. Delete or rename "casper-rw" to something else on the USB stick so your hard disk copy is used.
+
+4. At any time, you can copy your hard disk copy back onto the USB stick
+
+What to do in case of corruption and boot failure:
+--------------------------------------------------------
+You can either:
+1a- Copy your backed up "casper-rw" file onto the USB disk. You will lose your changed files since last backup.
+1b- Boot the USB stick by choosing a non-persistent boot option from the Ubuntu boot disk and perform a filesystem check. Once you get a terminal. Issue:
+$ sudo su -
+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.
+
+Installing Ubuntu completely on your hard drive for dual booting
+----------------------------------------------------------------
+1- Click on the "Install Ubuntu 11.04" link on the Desktop and follow the instructions.
+
+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
+
+.. 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>
+
+ .. image:: CC_by_3.0_88x31.png
+       :alt: Creative Commons License
+       :align: left
+       :target: http://creativecommons.org/licenses/by/3.0/
+
+ Live Comp Neurosci Ubuntu USB Stick by Cengiz Gunay is licensed under a `Creative Commons Attribution 3.0 Unported License <http://creativecommons.org/licenses/by/3.0/>`_.
+
+
+

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