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added posting from the mailing list as a wiki page
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‎_wikis/UsageAnalysis.md‎

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---
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title: UsageAnalysis
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---
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Usage Analysis
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--------------
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A question related to the discussion of how to design a future BioJava
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is to have a look at which parts of BioJava are being actively used and
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how to improve these.
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So what are the most frequently used bits of BioJava? One way to look at
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this is to go to the web-stats and see how many hits we have got on our
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documentation web pages.
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In an ideal world BioJava would be so simple to use, that nobody needs
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to read any docu. Unfortunately we are far away from this, so actually
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looking at these stats gives an impression on
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- topics / functionality which are of particular interest to the
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community
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- topics / functionality which might not be straightforward to use,
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therefore there are many hits on these pages.
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A look at the webstats from the last couple of months gives these top 10
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Cookbook pages that have been accessed frequently. This list is ordered
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by nr. of pageviews
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1. /wiki/BioJava:Cookbook:Alphabets
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2. /wiki/BioJava:CookBook:Blast:Parser
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3. /wiki/BioJava:Cookbook:SeqIO:ReadFasta
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4. /wiki/BioJava:Cookbook:SeqIO:ReadGES
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5. /wiki/BioJava:CookBook:DP:PairWise2
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6. /wiki/BioJava:CookBook:PDB:read
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7. /wiki/BioJava:Cookbook:Sequence
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8. /wiki/BioJava:Cookbook:SeqIO:WriteInFasta
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9. /wiki/BioJava:CookBook:Interfaces:ViewInGUI
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10. /wiki/BioJava:CookBook:Fasta:Parse
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Interpretation
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==============
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I would group these pages into 2 groups.
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A) How to work with core concepts of BioJava
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B) How to use a functionality of BioJava to achieve a certain goal
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Conceptual pages
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================
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The "conceptual" pages (A) I would identify as
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- How to get an Alphabet
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- How to make a Sequence Object from a String or make a Sequence
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Object back into a String
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Functionality pages
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===================
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The "functionality" pages (B) I would summarize as
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- How to parse a Blast output
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- How to read sequences from a Fasta file
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- How to read a GenBank, SwissProt or EMBL file
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- How to generate a global or local alignment with the
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Needleman-Wunsch- or the Smith-Waterman-algorithm
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- How to read a protein structure - PDB file
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- How to export a sequence to fasta
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- How to view a sequence in a gui
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- How to parse a Fasta database search output file
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As a conclusion I would suggest that BioJava should have the goal to
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provide easy access to the core "functionalities" (group B). I believe
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that we should try to keep the "concepts" that are being used to achieve
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these functionalities as simple as possible. In this sense, I feel that
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we have too many hits on the group A pages.

‎_wikis/UsageAnalysis.mediawiki‎

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== Usage Analysis ==
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A question related to the discussion of how to design a future BioJava is to have a look
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at which parts of BioJava are being actively used and how to improve these.
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So what are the most frequently used bits of BioJava? One way to look at this is to go to the
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web-stats and see how many hits we have got on our documentation web pages.
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In an ideal world BioJava would be so simple to use, that nobody needs to read any docu.
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Unfortunately we are far away from this, so actually looking at these stats gives an impression
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on
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* topics / functionality which are of particular interest to the community
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* topics / functionality which might not be straightforward to use, therefore there are many hits on these pages.
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A look at the webstats from the last couple of months gives these top 10 Cookbook pages that
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have been accessed frequently. This list is ordered by nr. of pageviews
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<pre>
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1. /wiki/BioJava:Cookbook:Alphabets
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2. /wiki/BioJava:CookBook:Blast:Parser
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3. /wiki/BioJava:Cookbook:SeqIO:ReadFasta
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4. /wiki/BioJava:Cookbook:SeqIO:ReadGES
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5. /wiki/BioJava:CookBook:DP:PairWise2
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6. /wiki/BioJava:CookBook:PDB:read
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7. /wiki/BioJava:Cookbook:Sequence
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8. /wiki/BioJava:Cookbook:SeqIO:WriteInFasta
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9. /wiki/BioJava:CookBook:Interfaces:ViewInGUI
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10. /wiki/BioJava:CookBook:Fasta:Parse
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</pre>
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= Interpretation =
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I would group these pages into 2 groups.
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<pre>
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A) How to work with core concepts of BioJava
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B) How to use a functionality of BioJava to achieve a certain goal
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</pre>
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=Conceptual pages=
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The "conceptual" pages (A) I would identify as
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* How to get an Alphabet
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* How to make a Sequence Object from a String or make a Sequence Object back into a String
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=Functionality pages=
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The "functionality" pages (B) I would summarize as
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* How to parse a Blast output
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* How to read sequences from a Fasta file
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* How to read a GenBank, SwissProt or EMBL file
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* How to generate a global or local alignment with the Needleman-Wunsch- or the Smith-Waterman-algorithm
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* How to read a protein structure - PDB file
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* How to export a sequence to fasta
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* How to view a sequence in a gui
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* How to parse a Fasta database search output file
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As a conclusion I would suggest that BioJava should have the goal to provide easy access to the
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core "functionalities" (group B). I believe that we should try to keep the "concepts" that are being used to
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achieve these functionalities as simple as possible. In this sense, I feel that we have too many hits on the group A pages.

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