[Bioperl-l] Database Retrieval

Chris Fields cjfields at uiuc.edu
Tue Aug 8 18:23:49 EDT 2006


I agree with "Don't get into the way of someone who threatens to code."  Not
my point by the response.  We are all willing to code here.  Sean has
donated preliminary code; I am willing to work on interfaces.  If Sendu
wants to work on this as well, fine, but indicate why he needs it by a
certain deadline.  I feel that forcing a deadline may be premature if the
sole reason (as Sendu indicated) is to include it in a possible 1.5.5
release, which, BTW, no one has stepped forward to make happen yet.

My main concern is 'turning people off' who want to contribute to Bioperl by
having a Bioperl developer (1) impose a deadline, and (2) indicate that they
will take things over if the deadline isn't reached.  That is, in essence,
what Sendu has done.  I had proposed making the deadline a few weeks later
as a compromise, to get Sean and I past the initial rush of the fall
semester.  I think this is perfectly reasonable. Sean's response also
indicates he is under time constraints as well.  And he indicates potential
problems, so any input (and code) he gives would be priceless.

Sendu never indicates why this can't wait a few extra weeks, just that he'll
dive in and do it himself anyway, regardless of what we think.  That's not
very considerate of Sean's efforts here, nor mine.  This is all completely
unintentional, I'm sure, (the medium of email does remove a certain
emotional quotient) but that's how it comes across, regardless.  At this
point, when I see things like this it makes me want to throw in the towel
and take a back seat to Bioperl development.  

I appreciate Sendu's intentions here, and I agree with him 99% of the time.
I listen to his opinions, and I hope he listens to mine.  And I understand
some of his reasoning in wanting to get this in ASAP; a new Bioperl release
is long LONG overdue.  I just don't want anyone's toes getting stepped on in
the process, especially someone willing to donate their own code, time, and
effort to help out.  The more hands the merrier (my point about this being a
community project), and Bioperl needs any help it can get right now.


> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Tuesday, August 08, 2006 4:32 PM
> To: Chris Fields; Sendu Bala
> Cc: bioperl-l at lists.open-bio.org list
> Subject: Re: [Bioperl-l] Database Retrieval
> Guys -
> we all remember the rule, don't we? "Don't get into the way of
> someone who threatens to code."
> Sendu may have his own time constraints under which he may have to
> deliver something. He wants to make that happen using and extending
> bioperl, building on the input and work of others. I can't see
> anything wrong with that, in fact I find it laudable, and I can't see
> why I would want to stop him or slow him down.
> I'm also sure that Sean will gladly welcome if somebody else does his
> work for him. At least I would.
> So please everybody take it easy.
> 	-hilmar
> On Aug 8, 2006, at 5:13 PM, Chris Fields wrote:
> > Sendu,
> >
> > As Sean and I both point out, we have time constraints during that
> > period.
> > We do have other priorities outside of Bioperl, as do most other
> > bioperl
> > contributors.  I'm glad that you have a lot of time to dedicate here;
> > Bioperl needs it.  But don't let that ambition drive away others
> > who want to
> > help.  This is a community project; don't forget that.
> >
> > My opinion: let Sean handle this for now.  You have plenty on your
> > plate as
> > it is.  Besides the huge Taxonomy issues to worry about, there is
> > also the
> > issue of a new developer point release that either you or I will
> > likely be
> > heading up.  Let that be your main focus at this point.  Sean can
> > handle
> > getting the basics going, then he'll likely ask for help when it
> > comes time
> > to get data into the right objects.
> >
> > Chris
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> >> Sent: Tuesday, August 08, 2006 3:06 PM
> >> To: bioperl-l at bioperl.org
> >> Subject: Re: [Bioperl-l] Database Retrieval
> >>
> >> Chris Fields wrote:
> >>> Sendu,
> >>>
> >>> 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.
> >>
> >> 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. I was planning to do this
> >> all by
> >> myself, so any ground work that gets done is a bonus for me. I don't,
> >> however, want it to be a hindrance (having to wait for it).
> >>
> >> For the DB interfaces, just putting out ideas and code snippets in
> >> this
> >> thread to promote discussion over the course of this month is
> >> probably
> >> most of the 'work' needed. Actually creating the modules after
> >> that is
> >> somewhat trivial.
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

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