[Biojava-l] UML diagrams for biojava tools?

[Bill Bug]

Hi Brian & Matthew,

I would definitely put in a vote for UML with BioJava.

UML *can* be a significant aid to accumulating requirements from around the
world and expediting their incorporation into a large framework like
BioJava.

I had just suggested an 'open systems' UML CASE tool - ArgoUML
(http://argouml.tigris.org/) - to Simon the other day.  As he mentioned,
there are commercial tools available - Rational being the most 'rational'
choice, given their functionality & level of integration with other commonly
used, SW engineering tools.  Many people may even get by with some of the
tools available in the Visio EE.

Still, I think the ArgoUML suite is awesome and does quite a 'reasonable'
job, reverse-engineering Use Case - and other diagrams - from java source &
javadocs.

That capability is crucial.  If the tool is to be useful in the long run,
the implementation & design engineers *must* be able to roll their
refactoring back into the requirements diagrams.  Without this capability,
the critical iterative component of the SW development process can't be
easily included in the UML documents.

I'm not certain how many bioinformatics folks are using UML, but I'm finding
it increasingly useful for complex development projects.  UML helps to
nurture the lines of communication between the functionality gurus defining
marketplace needs & requirements and the engineers designing, implementing &
testing the final product.

There is a reasonably steep learning curve getting up to speed in *using*
UML effectively.  However, if all players in the SW engineering & marketing
process learn to participate, the savings in time & wasted effort can be
great.  UML can help to maximize re-usability of all elements in the process
- not just classes & components - but all the usage & requirements analysis
documented as a part of a project.

Just my $0.02.

Keep up the great work on BioJava Matthew, Thomas & Simon.

Cheers,
Bill

Bill Bug
Ontological Engineer

DoubleTwist "Portal to the Code"
billb@doubletwist.com


-----Original Message-----
From: Matthew Pocock [mailto:mrp@sanger.ac.uk]
Sent: Wednesday, January 31, 2001 10:28 AM
To: Brian Gilman
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] UML diagrams for biojava tools?


Hi Brian,

Simon Brocklehurst very kindly ran the BioJava docs through something 
called 'Together' and posted the result at:

http://www.biojava.org/docs/uml/biojava-live/

It hasn't worked perfectly, and is slightly out of date now, but it 
shows what can be done. If people realy like this kind of display, then 
I guess we can see about improving it.

Matthew

Brian Gilman wrote:

> Hello all,
> 	
> 	Are you guys doing any UML diagramming? It would be nice to have a
> document showing all the relevent Interfaces and their relationships. 
> 
> 				Thanks!
> 
> 					-Brian Gilman
> 				
> -----------------------
> Brian Gilman <gilmanb@genome.wi.mit.edu>
> Software Engineer MIT/Whitehead Inst. Center for Genome Research
> One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
> phone +1 617  252 1069 / fax +1 617 252 1902
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
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