[Bioperl-l] Database Retrieval

Chris Fields cjfields at uiuc.edu
Tue Aug 8 21:09:56 EDT 2006

> My intent was to make clear you didn't have to do everything yourself,
> that help was available. I offered a solution to the deadline. If you're
> more comfortable working solo, that's entirely understandable. In which
> case another solution to the deadline is the one you already offered: to
> push it back or not have one.
> You offered your solution, I offered mine, we pick one and move on.
> Simple :)

That's not the way it came across, frankly.  In your own words:  

"I'm quite serious about the deadline; like I say, if you can't have it 
finished by then that's fine. You can commit what you have and I can 
take over toward the end of this month." 

This doesn't sound like you listened to my compromise, Sendu.  I proposed
moving the deadline back a few weeks (where I mentioned early to mid Sept)
to allow a little more breathing room for Sean and I; that's the compromise,
and I want to stick with that.  If it gets done early, fine.  If not, give
Sean a bit more time, until mid-Sept.  Then have at it.  

I was hoping an initial 1.5.5 release candidate would go out mid-Sept, a
second a week later, and the final one end-Sept.  This could be pushed back
a week to accommodate this if it's important to everybody (and, judging by
the level of interest, it is).

Anyway, by any means, a remedial UCSC DB class should be up-and-running by
mid-Sept at the latest, implementing Bio::DB::RandomAccessI to get Bio::SeqI
objects.  We could add in support for LocationI, ClusterI, and others along
the way if needed.  

An extra few weeks allows Sean time to add everything he wants and get the
general feel of Bioperl, so maybe he will have a few more ideas along the
way.  He has already indicated possible problems in his previous posts.  My
contribution here (interfaces) will be minor in comparison; I already have a
proto-LocationI interface, so others will take very little time and effort.
And, wouldn't it be great to have someone else contributing here?  Even if
it is small?  That's how a number of us started...

> As Hilmar supposed, I have my own deadlines; tying in with getting 1.5.5
> promptly out the door and inclusive of this proposal was icing on the
> cake. It's not the end of the world; if you both are interested in the

You need to actually state this when you demand a deadline.  We can't just
assume this!  It's a little off-putting to have someone you don't know very
well giving you deadlines to meet, esp. when they aren't your boss.  I
already have a P.I., thank you.  

> work and want to see it through to the end without help, that's super. I
> look forward to being able to use the code in the future. It just means
> I'll have to make other plans, so would like to know one way or the
> other toward the end of this month.

Give Sean some time.  Have a bit of patience!  An extended deadline allows
more input for 1.5.5 overall.  And anyone that wants to add ideas, have an
opinion, contribute code, make a suggestion along the way, with Sean's
contribution or with anything else, that's great!  That's what this is all

Not everybody here knows Bioperl as well as you, I, or Hilmar.  I believe in
the work you have contributed to Bioperl, Sendu.  I personally think you
should be the next Release Pumpkin, quite frankly; I just don't have time
right now.  But have some patience, man!  


More information about the Bioperl-l mailing list