X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=doc%2Fmanual%2Fmussagl_manual.rst;h=19b9690359cee9c742a041dc49c57066b4ab5324;hp=778e9abdd69a4f096d2f31c9db6378d6825eaa82;hb=9ef59dda76a5451e687feb030bf2b40634ea6ba9;hpb=0984be7e90435fbfc5209b88fc914a937add8a4e

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 778e9ab..19b9690 100644
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -10,6 +10,30 @@ Last updated: July 7th, 2006
 Updated to Mussagl build: 287
 
 
+.. Things to add
+	* New features / change log
+	* Comment out anything isn't implemented yet.
+	* List of features that will be implemented in the future.
+	* Look into the homology mapping of UCSC.
+        * Add toggle to genomes.
+        * Document why one fast record per region.
+        * How to deal with the hazards of small utrs vis motif finder. (Add warning)
+	* Add warning about saving fasta file.
+	* Add a general principles section near the top
+		* Using comparison algorithm which will pickup all repeats
+		* Add info about repeatmasking
+		* Checking upstream and downstream genes for make sure you are in the right regions.
+	* Later on: look into Ensembl
+	* Look into method of homology instead of blating.
+	* Mention advantages of using mupa.
+	* Mention the difference between using arrows and scroll bar
+	* Document the color for motifs
+	* Update for Mac user left click
+
+* Wormbase/Flybase/mirBASE
+
+
+
 .. contents::
 
 Introduction