[Biojava-l] some comments and wish list

Ewan Birney birney@ebi.ac.uk
Tue, 30 Jan 2001 09:10:08 +0000 (GMT)

On Mon, 29 Jan 2001, Matthew Pocock wrote:

> The flip side of this, is that we have been able to explore elegant 
> objects without the constraints of it having to work 24/7, so we are now 
> in a position to add lots of functionality to a relatively clean 
> framework (which doesn't have much inherant lava-flow design). I think 
> we trust our sequence object model to work & scale to the genomic and 
> into comparative-genomics without a lot of heart-ache - we have been 
> stress-testing by loading in the human genome this week - my 128mb pc 
> seems to handle this fine.

<grin> Is the assumption that Bioperl suffers from bad design and

I am actually impressed at the improvements made to the Bioperl design
frame work for the next branch, which I notice borrowed a quite a lot from
biojava for the location design.

Anyway, I *do* think that a more intergrative CORBA approach could allow
better leverage between the different projects. We'll have to see with the
new 0.2 BioCorba stuff and Bioperl 0.7 coming out whether this actually
works in-real-life.

> We are not stingey with read/write CVS access, so if you have code to 
> add, or wish to help maintain existing code, we are more than happy to 
> have you. A GAME parser would be great, as would any search program 
> parsers (either using the SAX-based parsers or the search result 
> objects). We realy are just the sum of our contributers.
> All the best,
> Matthew
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420