Made a few corrections to language in the main body of text. Changed the man...

Made a few corrections to language in the main body of text. Changed the man example to man echo instead of man man. Added a bit about tab autocompletion into the introduction. Rewrote and shortened the section on the Bio-IT Project. Removed mention of CMCI from the Centres section. Added some comments to Comments.txt.

linux_beginner/Comments.txt

@@ -41,3 +41,8 @@ Sonstige Probleme:
       try .. tabularcolumns::
       try using hack latex columns around two code blocks (-> Makefile)
   compile@Frank: references not set (example 4.6 Ensuring...)
+
+Added by Toby H, October 2015:
+- Rewritten & reduced the length of the section about the Bio-IT Project.
+- Removed the CMCI from the section about the EMBL Centres - it doesn't exist any longer.
+- Didn't have time to properly format (in bold, italic etc) the example commands, so have removed the mention of typographical conventions in the introduction. It is a good idea to have this formatting in place, though - I intend to go through and properly format eveything after the course this month.  

linux_beginner/about_bioit.rst

@@ -2,39 +2,18 @@
 About Bio-IT 
 -------------
 
-Bio-IT is a community project aiming to develop and strengthen the bioinformatics user community at EMBL Heidelberg. It is made up of members across the
-different EMBL Heidelberg units and core facilities. The project works to achieve these aims, firstly, by providing a forum for discussing and sharing
-information and ideas on computational biology and bioinformatics, focused on the `Bio-IT portal <http://bio-it.embl.de>`_. Secondly, we organise and
-participate in a range of different networking and social activities aiming to strengthen ties across the community.
+The Bio-IT Project aims to develop and strengthen the bioinformatics community at EMBL Heidelberg. It is made up of members across a range of disciplines in computational biology, in different Units and Core Facilities. The project aims to improve the standard of computational biology practised at EMBL Heidelberg, to encourage collaborations, and to provide a forum for discussion of issues and ideas relevant to bioinformatics here. 
+The activities of the project include::
+- the organisation and delivery of training courses such as this one
+- the provision of one-to-one training and consultancy
+- the organisation of social and networking events for the computational biology community
+- regular meetings to discuss issues and ideas
+- the development and maintenance of the Bio-IT Portal <http://bio-it.embl.de>
 
-Resources 
-^^^^^^^^^^
+The Portal hosts information regarding upcoming courses and conferences/other events relevant to computational biology, resources to help with your work, and profiles of people involved in bioinformatics at EMBL. It is accessible from within the EMBL network (you must connect via VPN for off-site access).
 
-A list of biocomputing-related resources associated with the project, including, for example help provided for installing software on Linux computers
-at EMBL, instructions on using the Git versions control system server provided by EMBL, and various other kinds of information. 
 
-Training and Outreach 
-^^^^^^^^^^^^^^^^^^^^^^
-
-Bio-IT provides information on events (courses and conferences), both internal to EMBL and organised elsewhere by other organisations, that are related to
-biocomputing and bioinformatics.
-
-Networking 
-^^^^^^^^^^^
-
-Several different kinds of networking events for the Bio-IT community are being organised, including beer sessions for the EMBL community, and within-Heidelberg
-events for the larger Heidelberg biocomputing community.
-
-Biocomputing expertise at EMBL 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-You can use the Bio-IT portal to search for people working at EMBL who have experience working with data or tools you might be interested in. 
-
-If you've not yet got a page up on the portal describing your own expertise, please do so. If you need any help doing this, you can read about this in the
-portal's FAQ section, or get in touch with one of the site administrators.
-
-
-Centers
+Centres
 ^^^^^^^
 `EMBL Centres <http://www.embl.de/research/interdisciplinary_research/centres/index.html>`_ are 'horizontal', 
 cross-departmental structures that promote innovative research projects across disciplines. All the EMBL Centres listed below
@@ -50,11 +29,6 @@ have a strong computational component.
    :alt: CSDA
    :target: http://bio-it.embl.de/statistical-data-analysis
 
-.. |cmci| image:: _static/img-cmci.jpg
-   :width: 20%
-   :alt: CMCI
-   :target: http://bio-it.embl.de/molecular-and-cellular-imaging
-
 .. |cbm| image:: _static/img-cbm.jpg
    :width: 20%
    :alt: CBM
@@ -72,11 +46,6 @@ Statistical Data Analysis
 
 The `CSDA <http://bio-it.embl.de/statistical-data-analysis>`_ helps EMBL scientists to use adequate statistical methods for their specific technological or biological applications.
 
-Molecular and Cellular Imaging
-""""""""""""""""""""""""""""""
-
-The `CMCI <http://bio-it.embl.de/molecular-and-cellular-imaging>`_ makes your life in image processing/analysis easier and more fun.
-
 Modeling
 """"""""
 

linux_beginner/conf.py

@@ -39,7 +39,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'Introduction to the Linux Commandline'
-copyright = u'2012,2013,2014, Holger Dinkel & Frank Thommen'
+copyright = u'2012,2013,2014,2015 Holger Dinkel, Frank Thommen & Toby Hodges'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

linux_beginner/introduction.rst

@@ -7,7 +7,7 @@ Why Use the Commandline
 ***********************
 
 - It's **fast**. Productivity is a word that gets tossed around a lot by so-called power users, but the command line can
-  really streamline your computer use, assuming you learn to use it right.
+  really streamline your computer use, assuming you learn to use it correctly.
 
 - It's **easier to get help**. The command line may not be the easiest thing to use, but it makes life a whole lot
   easier for people trying to help you and for yourself when looking for help, especially over the internet. Many times
@@ -49,7 +49,7 @@ General Remarks Regarding Using UNIX/Linux Systems
 .. _figure-filesystem:
 .. figure:: _static/filesystem.png
 
-  Depending on the Linux distribution you might or might not find all of above
+  Depending on the Linux distribution you might or might not find all of the above
   directories. Most important directories for you are ``/bin`` and ``/usr/bin``
   (sometimes also ``/usr/local/bin``) which contain the user software, ``/home`` which
   usually contains the users' homedirectories and ``/tmp`` which can be used to store
@@ -63,17 +63,17 @@ Absolute Paths / Relative Paths
 A path describes the location of a file/folder in the filesystem: 
 It is important to understand that there are basically two ways to describe such a path: Either by using an *absolute* pathname, or by using a
 *relative* pathname. The difference is that *absolute* paths always start with a "slash ``/``". This "slash" denotes the so called "root" of the
-filesystem (see below). *Relative* paths in contrast always starting with a directory name and denote the location of a file/folder *relative* to
+filesystem (see below). *Relative* paths in contrast always start with a directory name and denote the location of a file/folder *relative* to
 the current directory.
 
 .. note:: When in doubt, it's best to use *absolute* filenames. Commands given with absolute pathname are more easily repeated later, as they can
-   be run independent of the current working directory (unlike relative paths).
+   be run regardless of the current working directory (unlike relative paths).
 
 ***********************************
 General Structure of Linux Commands
 ***********************************
 
-:index:`Many <command; general structure>` linux commands have options and accept arguments. Options are a set of switch-like parameters
+:index:`Many <command; general structure>` Linux commands have options and accept arguments. Options are a set of switch-like parameters
 while arguments are usually free text input (such as a filename).
 
 .. figure:: _static/LinuxCommandStructure.png
@@ -97,7 +97,7 @@ Short options are usually - though not always - concatenatable:
   $ ls -l -A -h
   $ ls -lAh
 
-Some options require an additional argument, which is added with a blank to the short form and with an equal sign to the long form:
+Some options require an additional argument, which is added after a blank to the short form and an equal sign to the long form:
 
  :: 
 
@@ -121,7 +121,6 @@ A Journey Through the Commands
 
 Please note that all examples and usage instructions below are just a glimpse of what you can do and reflect our opinion on what's important and what's not. Most of these commands support many more options and different usages. Consult the manpages to find them.
 
-Typographical conventions: Commands and examples are written in Courier.  User Input is written in Courier bold and placeholders are generally written in italic.
 
 Useful Terminal Tools & Keyboard Shortcuts
 ==========================================
@@ -138,6 +137,11 @@ On most Linux systems you can use the mouse to select text and then press the mi
 paste that text at the position where your cursor is. This is especially useful for long directory
 or filenames.
 
+Saving time/avoiding typos with autocompletion
+----------------------------------------------
+
+On most Linux systems you can autocomplete command names and filepaths by pressing :kbd:`TAB`. This looks at the characters that you have entered so far and tries to predict what the rest of the command/path will be. This can save you from having to type out long command and file/directory names, and also reduces the likelihood of you accidentally spelling something incorrectly.
+
 
 Printing some text
 ------------------
@@ -208,7 +212,7 @@ Getting Help
 -----------------------------------
 
 Many commands support a "help" option, either through ``-h`` or through ``--help``. 
-Other commands will show a help page or at least a short usage overview if you provide incorrect commandline options
+Other commands will show a help page or at least a short usage overview if you provide incorrect commandline options.
 
 :index:`man` - show the manual page of a command
 ------------------------------------------------
@@ -218,20 +222,21 @@ Other commands will show a help page or at least a short usage overview if you p
 
  :: 
 
-  $ man man
-  man(1)
+  $ man echo
+  echo(1)
   
   NAME
-   man - format and display the on-line manual pages
+         echo - display a line of text
   
   SYNOPSIS
-   man [-acdfFhkKtwW] [--path] [-m system] [-p string] [-C config_file]
-  ...
+         echo [SHORT-OPTION]... [STRING]...
+         echo LONG-OPTION
+    ...
   $
 
 For the navigation within a manpage and how to exit the manpage, see the :ref:`paragraph regarding less <less>`.
 
-.. note:: The behaviour of ``man`` is dependent of the ``$PAGER`` environment variable
+.. note:: The behaviour of ``man`` is dependent of the ``$PAGER`` environment variable.
 
 :index:`apropos` - list manpages containing a keyword in their description
 --------------------------------------------------------------------------
@@ -247,13 +252,13 @@ For the navigation within a manpage and how to exit the manpage, see the :ref:`p
   whoami               (1)  - print effective userid
   $
 
-Use ``apropos`` to find candidates for specific tasks
+Use ``apropos`` to find candidates for specific tasks.
 
 
 /usr/share/doc/
 ---------------
 
-The ``/usr/share/doc/`` directory in some Linux distributions contains additional documentation of installed software packages 
+The ``/usr/share/doc/`` directory in some Linux distributions contains additional documentation of installed software packages. 
 
 Who am I, where am I
 ====================
@@ -329,7 +334,7 @@ Moving Around
   $
 
 .. note:: Using ``cd`` without a directory is equivalent to "``cd ~``" and changes into the users's homedirectory
-.. note:: Please note the difference between absolute paths (starting with "``/``") and relative paths (starting with a directory name)
+.. note:: Please note the difference between absolute paths (starting with "``/``") and relative paths (starting with a directory name).
 
 Special directories:
 
@@ -462,7 +467,9 @@ If the last filename given is nonexisting then the first file is copied as this
   $ cp /usr/bin/less /tmp/
   $
 
-If, however, the last filename given is an (existing!) directory, then the file is copied into this directory: :: 
+Be careful! If the last filename given does exist, this file will be overwritten and replaced with a copy of the first file.
+
+If the last filename given is an (existing!) directory, then the file is copied into this directory: :: 
 
   $ cp /usr/bin/less /tmp/
   $
@@ -489,7 +496,7 @@ To recursively copy files, we need to specify the ``-r`` option. Here, we copy a
   ...
   $
 
-``rsync`` allows you to copy files or folders locally or to wherever you have ``ssh`` access.  You can have ``rsync`` have copying only newer files or only older files.  If copy operation is interrupted, you can rerun ``rsync`` and it will only copy the missing files (in contrast to ``cp`` which will just copy everything again).
+``rsync`` allows you to copy files or folders locally or to wherever you have ``ssh`` access.  You can have ``rsync`` copy only newer files or only older files.  If copy operation is interrupted, you can rerun ``rsync`` and it will only copy the missing files (in contrast to ``cp`` which will just copy everything again).
 
 ``source`` and ``target`` can be local directories or have the form ``user@remotehost:directory``, in which case you'll have to give your password for the remote host.  This latter version will copy over the network.