[Bioperl-l] Database Retrieval

Chris Fields cjfields at uiuc.edu
Tue Aug 8 15:47:49 EDT 2006


I hate to say this, but rethink that deadline a little.  Sept 4 falls at the
beginning of the academic year so I will be flooded with tons of work, let
alone work on $job (postdoc, bench scientist) and try to get EUtilities in
decent shape.  So I'm doing some heavy prioritizing now; this falls further
down on the list.

It's probably the same on Sean's end as well.  Hence my thought that getting
Sean a CVS account would speed things along.  

It would be nice to get 1.5.5 out by late Sept-mid Oct.  But we also need to
be realistic. 

I think a basic UCSC sequence retrieval implementation using RandomAccessI
and Sean's code is doable by early to mid-September.  Again, the backend
data retrieval component is the critical part here.  I'm working on the
interfaces for other data, but that will take shape once I have a better
idea of the data that's available.  Hilmar suggested LocationI and
Annotation::Reference as a start; any other suggestions?


> Sean Davis wrote:
> >
> > On 8/8/06 12:53 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
> >
> >> Should Sean get an CVS account or should we just pass everything via
> >> a proxy, Sendu maybe?  Might be easier to give him CVS access so
> >> Sendu can focus on Taxonomy, I can focus on the interfaces and
> >> getting through my benchwork (?!?), and Hilmar can focus on $job.
> >
> > Whatever works for me, although I should probably run stuff by folks
> first,
> > as I'm not used to the bioperl conventions--errors, etc....
> I've placed this 'project' as a point for the 1.5.5 bioperl release
> currently planned for 'fall 2006'. But so you both have a better idea of
> time-lines, here's a very aggressive one for you:
> I'm going to want to start using, or start writing, a front-end
> module(s) on September 4th.
> So ideally I'd like to see the backend and interface work done before
> then. As we get closer to the end of the month, if it doesn't seem like
> that's going to happen, let me know and I can dive in and start helping
> out directly on those areas.
> Thank you,
> Sendu.
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