test/data/vclamp_jpk/README: Document sample versions

[hooke.git] / doc / index.txt

diff --git a/doc/index.txt b/doc/index.txt
index 2225fcccfc2695fd3e6c44f952c4ab520afb2167..a067fb7f6731b1b4ae324ff0a1ec4e8a9ec1b754 100644 (file)
--- a/doc/index.txt
+++ b/doc/index.txt
@@ -1,5 +1,5 @@
-Welcome to the Hooke documentation!
-===================================
+Welcome
+=======
 
 Hooke_ is software for the (semiautomatic) analysis and filtering of
 force curves.  Force curves are the output of an analytical technique
@@ -20,60 +20,48 @@ Features:
 * Handles force-clamp force experiments (experimental)
 * Extensible by users by mean of plugins and drivers 
 
-Contents:
+Contents
+========
 
 .. toctree::
    :maxdepth: 2
 
    install
    tutorial
+   analysis
    config
+   bugs
    hacking
+   standards
    hooke/hooke
    doc
 
 Indices and tables
-==================
+------------------
 
-* :ref:`~genindex`
-* :ref:`~modindex`
-* :ref:`~search`
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. todolist::
 
 Publications
 ============
 
-Hooke has been published [1]. Please cite Hooke if you use it.  Let us
-know, and we'll link to your paper!
+Hooke has been published [#sandal2009]_. Please cite Hooke if you use
+it.  Let us know, and we'll link to your paper!
 
 
-[1] Sandal M, Benedetti F, Brucale M, Gomez-Casado A, Samorì B.,
+.. [#sandal2009] M. Sandal, F. Benedetti, M. Brucale, A. Gomez-Casado,
+  B. Samorì.
   "Hooke: an open software platform for force spectroscopy."
   Bioinformatics, 2009.
   doi: `10.1093/bioinformatics/btp180 <http://dx.doi.org/10.1093/bioinformatics/btp180>`_
 
-
-Troubleshooting
-===============
-
-If you have troubles in using Hooke:
-
-1. Search the `issue tracker`_.
-2. Look at the `trouble shooting wiki page`_.
-3. Search the `discussion group`_.
-4. Ask a question in the discussion group.
-5. File a bug on the issue tracker.
-
-.. _issue tracker: http://code.google.com/p/hooke/issues/list
-.. _trouble shooting wiki page:
-   http://code.google.com/p/hooke/wiki/TroubleShooting
-.. _discussion group: http://groups.google.com/group/hookesoftware
-
-
 Disclaimer
 ==========
 
 Remember that Hooke is still experimental software!  It has been
 mostly done to fit the needs of its authors, and there is no guarantee
 it will do what you need.  However, you can write us/help us improve
-it so that it does.  We aim to make of Hooke a little, universal tool
-that can help your research.
+it so that it does.