[Bioperl-l] distant thoughts from a dinosaur...

[Ewan Birney]

I have read with some interest the rest of the bioCPAN threads and the
proposal from Nat to review Bioperl. This jives alot with discussions
happening closer to the core about redesigning parts of bioperl for
cleaner handling of a number of things.


These things I think are great. They all show the maturity of Bioperl
and it is also great to see new people start to really come forward
and play a bigger role. For what it is worth, here is my view:


(a) I think BioCPAN is a great idea and is needed for all three
catagories of tasks - Bioperl related but not "quality controlled"
bioperl stuff, Bioperl stuff in the "alpha" stage and being tried
out and finally breaking Bioperl down from being monolithic to
being Bundle-orientated.


  - Whatever technical solution sounds best is great. Go for
it Nat/Heikki whoever...


(b) Review and revision of Bioperl. Bioperl probably really needs
this, and this is a healthy thing. I think we should be honest
with ourselves and call it Bioperl 2.0, because that is what it
will be (remember - first version number indicates rough API
concordance, second number means is strict API concordance, with
assumme "drop-in" upgrades for different third numbers).


  Bioperl 2.0 in my view ----

    --- should be designed by with reference to the success and
mistakes and Bioperl 1.x. I think the two outright successes have been
SeqIO and SearchIO --- mistakes I think is probably the sort of
somewhat tangled mess we got into in features/locations/feature
holders/"big" sequence object stuff. The DB stuff is also ugly
compared to SeqIO/SearchIO. Most people agree that we have blended two
or three ideas in our "Interface" files which maybe should be
unblended or we should decide what we are doing anyway.

    --- I think Nat's idea of an orderly review by someone, like
SteveC is very sane and would start this process off nicely.

    --- should be designed in a iterative fashion of discussion,
working code proposal (early on) prototypes (mid way) moving quickly
to real skeletons which are expected to last a long time. We should
avoid a massive navel-gazing exercise with no code.

    --- We are bound to have a proposal to change the start from
1 to 0 of sequences. We should have some reasoned discussion and
then vote/or leave to the leader's taste (I prefer the latter...)

    --- should be actively lead by one or a very small number of
people who have serious bioinformatics experience

    --- who should **not** be me, as I am clearly going to be happy as a
pig in mud with the Bioperl 1.x series for a long long time ;), I am
a dinosaur compared to some of the young-crazy-boys-and-girls out there
and will probably be coding $seq->trunc($start,$end)->revcom() for
the rest of life...


    --- *my* (personal choice!) favourites for the person or the small
cabal would be one of Aaron and Heikki, but I do feel that anyone who
made good suggestions and ended up doing the work can just as easily
be a good person to lead this --- it is just that I haven't got to
know them yet!. Jason would also be excellent, but he's got to
concentrate on his PhD (US PhDs are too long anyway without
encouragement), and I'll sit on him if he spends too much time on
Bioperl <grin>. ChrisM would also be a great person, but he has alot
on his plate; Lincoln would be great but he **really** has too much on
his plate (don't even think it Lincoln); Hilmar would also be great
but I strongly suspect he'd say no ;). I would trust Elia if we wanted
to do this (fancy it Elia?); Paul E as well as a new outsider might
work out well, but I haven't actively used much of his code. Anyone else
- and I do mean **anyone** could be the focal point if he/she got the
trust of us as a community...


   --- I would claim that the main thing we should take from Bioperl is
community and culture; being:

    - community of people who do real-life bioinformatics in Perl

    - culture being open with

        - anybody can join; anybody can lead. You prove
          yourself by your comments on the list and the
          code/documentation you provide

        - whoever codes it wins the argument
           aka:
        - working code trumps abstract arguments

        - we should live up to our promises as much as
          possible for:
             - testing as much as possible
             - documenting sensibly
             - bug finding and fixing as much as possible
             - stability of API when we say it is stable



So... my rather grandiose thoughts. I'd love to see Bioperl 2.0
set sail, and it gives me the warm-fuzzies that we can discuss
all this with such a large and diverse community. Whey hey!



ewan