Congratulations!  You have successfully installed the TOPP tools of OpenMS and
the OpenMS library.

"TOPP" is an acronym for "The OpenMS Proteomics Pipeline".  It consists of
several small applications that can be chained to create analysis pipelines
tailored for a specific problem.

Note that the Windows binary release is meant for end-users only, rather than
for developers who want to contribute algorithms.  Developers should download
the source code version (see http://www.open-ms.de for details).

======================
Read the documentation
======================
To get familiar with TOPP we recommend reading the documentation.  Look into
your Start-Menu (Start - Programs - OpenMS) and open the Documentation page.
On the left side you will see the TOPP section.  Read it after finishing with
this document! Ignore any technical details; these are meant for developers.
Especially you should read the "TOPP tutorial" and "TOPP documentation".

The TOPP tools can be called from two graphical
applications (GUI) which are part of this installation; either "TOPPView", or "TOPPAS".
See the documentation for a tutorial on how to use TOPPView and TOPPAS.
Pipelines can also be created this way.
Advanced users can also use scripts and the Windows command line. Pipelines can be run from 
a GUI tool or via the "ExecutePipeline" command line tool.

The INIFileEditor allows you to edit .ini-Files, which are XML configuration
files that every TOPP tool can use to adjust its parameters.

========================
The Windows command line
========================

This part is usually not neccessary for the common user, even if you are advanced.
However, special requirements (e.g. automated conversion tools, webserver or cluster integration)
might require you to use the command line.
To get familiar with the Windows command line, we recommend reading one of
many tutorials available on the internet
(e.g. http://www.voidspace.org.uk/python/articles/command_line.shtml).  The
most useful command you will need are 'cd' (change into a directory) and 'dir'
(list the content of the current directory).  You can get further information
on those commands by typing "help cd" or "help dir".  Typing "help" alone will
give you all available commands.  You will find a link in the OpenMS start
menu group, which opens a Windows command line.  Once the command line is
open, you can type 'dir' to see the names of the TOPP tools, which reside in
the directory.  You can just call a TOPP tool without any further arguments -
it will print some useful information and give you hints on how to use the
TOPP tool.  Note that you can call the TOPP tools from any directory, i.e. you
do not have to be in "C:\program files\OpenMS\TOPP" to call the FeatureFinder
tool.


