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

Heikki Lehvaslaiho heikki at nildram.co.uk
Mon Jul 7 21:55:20 EDT 2003


That really sounded like a testament. Text worth saving and rereading. I
hope you are not too far gone! Is it just two weeks without email?

I do to take part in taking bioperl over to version 2, but I think my
vision at the moment is too limited to take the lead.

I was hoping that Nat's investigation of BioPAN would have provided a
more detailed insight into various possibilities of taking bioperl
forward. For the time being, I think I better concentrate into smaller,
better focused projects.

That clear, objective review of the current bioperl from someone not too
closely  involved with the project is definitely the way to start.
Volunteers? More than one?


On Mon, 2003-07-07 at 19:22, Ewan Birney wrote:
> 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
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