Mussa Manual: Todo comments

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 778e9abdd69a4f096d2f31c9db6378d6825eaa82..19b9690359cee9c742a041dc49c57066b4ab5324 100644 (file)
--- 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