X-Git-Url: http://git.tremily.us/?a=blobdiff_plain;f=doc%2Findex.txt;h=a067fb7f6731b1b4ae324ff0a1ec4e8a9ec1b754;hb=422d2dc8798f25d64f2a27dd258bdcbb45df4d60;hp=3e88c31f3f5878553b072af6fd2e5a8275ce7809;hpb=7ba5f553f8344edb31a72576d5fbade55516e9b4;p=hooke.git

diff --git a/doc/index.txt b/doc/index.txt
index 3e88c31..a067fb7 100644
--- 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.txt
-   tutorial.txt
-   config.txt
-   hacking.txt
-   hooke/hooke.txt
-   doc.txt
+   install
+   tutorial
+   analysis
+   config
+   bugs
+   hacking
+   standards
+   hooke/hooke
+   doc
 
 Indices and tables
-==================
+------------------
 
 * :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.
+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.