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

[Richard Holland]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

would you mind if i posted your comments to the wiki but without your name?

that way everyone can read and comment as needed, but any politics
involved with who said what are avoided.

cheers,
Richard

Michael Heuer wrote:
> 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:
> 
> 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)
> ----
> 
>>

> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.2.2 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFHMFGT4C5LeMEKA/QRAkneAJ9TIRn8U9Bpmdt45R9UwV2ZrL3dcwCgmIcq
SPkJmxfthlyTgbajDv9/lDc=
=zpQK
-----END PGP SIGNATURE-----