[Biojava-dev] The future of BioJava

[Richard Holland]

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I totally agree.

Can you post a short summary of this to the Wiki page?

Not all aspects of BioJava are documented, leading people either to give
up, consult the JavaDocs online, or post a message to biojava-l or
biojava-dev.

Is it possible to get similar stats to the ones you have calculated for
the JavaDoc pages on our website?

Also, is it possible to build some kind of index over the mailing list
archives to pull out the most frequently used terms?

cheers,
Richard

Andreas Prlic wrote:
> Hi,
> 
> A question related to the discussion of how to design a future BioJava
> is to have a look
> at which parts of BioJava are being actively used and how to improve these.
> 
> So what are the most frequently used bits of BioJava? One way to look at
> this is to go to the
> web-stats and see how many hits we have got on our documentation web pages.
> 
> In an ideal world BioJava would be so simple to use, that nobody needs
> to read any docu.
> Unfortunately we are far away from this, so actually looking at these
> stats gives an impression
> on
> 
> * topics / functionality which are of particular interest to the community
> * topics / functionality which might not be straightforward to use,
> therefore there are many hits on these pages.
> 
> A look at the webstats from the last couple of months gives these top 10
> Cookbook pages that
> have been accessed frequently. This list is ordered by nr. of  pageviews
> 
> 1. /wiki/BioJava:Cookbook:Alphabets
> 2. /wiki/BioJava:CookBook:Blast:Parser
> 3. /wiki/BioJava:Cookbook:SeqIO:ReadFasta
> 4. /wiki/BioJava:Cookbook:SeqIO:ReadGES
> 5. /wiki/BioJava:CookBook:DP:PairWise2
> 6. /wiki/BioJava:CookBook:PDB:read
> 7. /wiki/BioJava:Cookbook:Sequence
> 8. /wiki/BioJava:Cookbook:SeqIO:WriteInFasta
> 9. /wiki/BioJava:CookBook:Interfaces:ViewInGUI
> 10. /wiki/BioJava:CookBook:Fasta:Parse
> 
> I would group these pages into 2 groups.
> A) How to work with core concepts of BioJava
> B) How to use a functionality of BioJava to achieve a certain goal
> 
> The "conceptual" pages (A) I would identify as
> * How to get an Alphabet
> * How to make a Sequence Object from a String or make a Sequence Object
> back into a String
> 
> The "functionality"  pages (B) I would summarize as
> * 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
> 
> 
> As a conclusion I would suggest that BioJava should have the goal to
> provide easy access to the
> core "functionalities" (group B).  I believe that we should try to keep
> the "concepts" that are being used to
> achieve these functionalities as simple as possible. In this sense, I
> feel that we have too many hits on the group A pages.
> 
> Andreas
> 
> -----------------------------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                               Hinxton, Cambridge CB10 1SA, UK
>              +44 (0) 1223 49 6891
> 
> -----------------------------------------------------------------------
> 
> 
> 
> --The Wellcome Trust Sanger Institute is operated by Genome
> ResearchLimited, a charity registered in England with number 1021457 and
> acompany registered in England with number 2742969, whose
> registeredoffice is 215 Euston Road, London, NW1 2BE.
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