[Biojava-dev] [Fwd: BioJava 3 Proposal]

[Michael Heuer]

Hello Richard,

I'm not sure if I want any of this up on the wiki, but here are a few
of my thoughts...

Immutable classes, not beans, are the safest and most efficient.

Statements like "We would adhere rigidly to a common coding style and
heavily comment the code." only work if there is a way to measure and
enforce it.  A better way to say this would be something like "All
committed code must have zero style errors as measured by Checkstyle with
our local checkstyle configuration, have zero coding errors as measured by
FindBugs with our local findbugs configuration, have 95% unit test
coverage as measured by Cobertura", and so on.

Sequence features aught to align with the Sequence Ontology (SO/SOFA).
The two top-level sequence feature types are Region (SO:0000001, "A
sequence_feature with an extent greater than zero.") and Junction
(SO:0000699, "A sequence_feature with an extent of zero.").

Is there a role for biojava in any of

Ontologies in OBO format
Ontologies in OWL format
BioPAX
MAGE-ML/SOFT/MINiML
FuGO/OBI
SMBL/CellML
Web services/BioMoby
etc.

or is each best handled by their respective projects/tools?

   michael


Richard Holland wrote:

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> Hi all. I'm planning on opening this wiki page to the general public
> (ie. biojava-l) on Monday next week (Oct 29th). The email that will
> accompany the public announcement is shown below.
>
> If you'd like to review it and add any further comments or suggestions
> before everyone else gets to see it, please make those changes before
> this coming weekend is over!
>
> The page will be made visible as-is, and will be left open for public
> comment until January when I will distribute a summary of its contents
> and start work on a plan of action.
>
> cheers,
> Richard
>
> Here is the email that will be sent out on Monday:
>
> - ----
> Dear BioJava users,
>
> The BioJava developers are considering options for the future
> development of the BioJava toolkit. We consider that it needs
> improvement in a few major areas to make it easier to use and
> understand, and also faster and more scalable.
>
> The options are to either rewrite large parts of the existing code,
> working within the existing interfaces and paradigms, or to develop a
> new set of BioJava packages from the ground up in order to take
> advantage of lessons learned from the design patterns of the existing code.
>
> The BioJava developers have spent the last couple of months discussing
> ideas and proposals related to these options on a Wiki page, and would
> now like to open this discussion to all users of BioJava and the
> bioinformatics community in general. We would like to invite anyone who
> has any ideas or suggestions to contribute these to the Wiki page,
> and/or to comment on the ideas and suggestions that have already been
> posted there.
>
> Here is a link to the Wiki page, and also a link to the associated Talk
> page where much of the discussion has taken place so far:
>
> 	http://biojava.org/wiki/BioJava3_Proposal
> 	http://biojava.org/wiki/Talk:BioJava3_Proposal
>
> It is our intention to leave the discussion open until early January
> 2008 when we will summarise it and use it as the basis of a plan of
> action. We will then distribute the summary and the action plan via the
> BioJava website.
>
> We look forward to hearing your comments and ideas. Please do remember
> to make them directly to the Wiki page so that they are preserved in
> context, making it easier for us to summarise them later!
>
> cheers,
> Richard
> (on behalf of all BioJava developers)
> - ----
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