Change to wiki page

Andrewyatz · andreasprlic · commit f982d2897828 · 2016-04-09T10:57:49.000-07:00
diff --git a/_wikis/BioJava3_Proposal.md b/_wikis/BioJava3_Proposal.md
@@ -107,3 +107,32 @@ Action plan
 2.  Tentative Singapore meeting to get the ball rolling on the final
     design and initial coding front.
 
+Categories of Improvement
+-------------------------
+
+Initally suggested by Andreas this attempts to group the currently
+recognized *issues* surrounding Biojava.
+
+### Category A
+
+How to work with core concepts of BioJava:
+
+-   How to get an Alphabet
+-   How to make a Sequence Object from a String or make a Sequence
+    Object back into a String
+
+### Category B
+
+Functionality; taking on concepts/practices from *Category A* and
+applying them to a bioinformatics problem.
+
+-   How to parse a Blast output
+-   How to read sequences from a Fasta file
+-   How to read a GenBank, SwissProt or EMBL file
+-   How to generate a global or local alignment with the
+    Needleman-Wunsch or the Smith-Waterman-algorithm
+-   How to read a protein structure - PDB file
+-   How to export a sequence to fasta
+-   How to view a sequence in a gui
+-   How to parse a Fasta database search output file
+
diff --git a/_wikis/BioJava3_Proposal.mediawiki b/_wikis/BioJava3_Proposal.mediawiki
@@ -39,4 +39,28 @@ It is suggested that development stop on the existing BioJava/BioJavaX/BioJava2
 ==Action plan==
 
 # Please modify this page and the [[Talk:BioJava3_Proposal|Talk page]] as you see fit in order to flesh out details and/or make new points.
-# Tentative Singapore meeting to get the ball rolling on the final design and initial coding front.
+# Tentative Singapore meeting to get the ball rolling on the final design and initial coding front.
+
+==Categories of Improvement==
+
+Initally suggested by Andreas this attempts to group the currently recognized ''issues'' surrounding Biojava.
+
+===Category A===
+
+How to work with core concepts of BioJava:
+
+* How to get an Alphabet
+* How to make a Sequence Object from a String or make a Sequence Object back into a String
+
+===Category B===
+
+Functionality; taking on concepts/practices from ''Category A'' and applying them to a bioinformatics problem.
+
+* How to parse a Blast output
+* How to read sequences from a Fasta file
+* How to read a GenBank, SwissProt or EMBL file
+* How to generate a global or local alignment with the Needleman-Wunsch or the Smith-Waterman-algorithm
+* How to read a protein structure - PDB file
+* How to export a sequence to fasta
+* How to view a sequence in a gui
+* How to parse a Fasta database search output file
