To come back to this: I am basically on the enumerator-side of things right now. It is a bit strange as IterIO seems to have such a nice, clean interface, but since ~50 packages are already using enumerator, it is probably the one that is most future-proof.
One problem I have is that a number of interesting features are missing;
the one I find most useful is iteratee's zip (zip3, ...). Oh and arrow
instances ;-)
What I am not sure of, is if each data source (say, reading fasta files)
should be in its own library (giving us s.th. like 20 small libraries)
or if one big blob would be better?
Gruss,
Christian
* Ketil Malde <ke...@malde.org> [09.06.2011 12:21]:
>
> At least Christian and I are going to ISMB/ECCB, and the preceeding BOSC
> and 'codefest' - i.e. a bioinformatics hackathon. We should start
> thinking of some tasks to address, and there's a common document for the
> codefest (see attached main from Brad Chapman).
>
> Some things I'd be interested in:
>
> * Separating out a bio-core library. There is a bit of overlap
> between the different libraries, I think there's a market for a
> small common library with the most common, shared, data
> definitions.
> * benchmarking the bio library. I used to have a hacked quickcheck
> for this, but it doesn't work after moving to QC2. A better
> approach is to use criterion for this.
> * Iteratee-based parsing and analysis. I really need to experiment
> with iteratees and enumerators to get a better feel for how they
> work in practice. This is likely to be more a learning
> experience than resulting in useful code, but who knows?
> * Cleaning up parser interfaces. Unless we decide to move
> everything to iteratees, I'd like all file formats in bio
> to follow the '{de,en}codeFoo,{read,write}Foo'(etc) pattern.
>
> And of course, the perennial task of improving documentation and adding
> test cases...
>
> Also, broadening our horizons a little:
>
> * Look into packaging of libraries and applications (rpms and debs),
> especially 'flower' and 'flowsim', but perhaps others as well.
> * Integrate applications with Galaxy or other platforms.
>
> This is just some stuff I thought of, doubtlessly I've missed many
> important and interesting things, so please suggest or vote for whatever
> tasks you prefer to see worked on!
>
> -k
>
> Date: Wed, 8 Jun 2011 15:23:41 -0400
> From: Brad Chapman <chapm...@50mail.com>
> To: openbio-codefest2...@googlegroups.com
> Subject: [codefest] Codefest 2011 initial planning
>
> Hello everyone;
> Thanks so much for signing up for Codefest 2011. I'm thrilled to see
> so many interested developers and am looking forward to a fun two
> days of coding:
>
> http://www.open-bio.org/wiki/Codefest_2011
>
> This mailing list is setup to help facilitate introductions and
> discussions leading up to our trip to Vienna. The work and content
> of Codefest is completely dictated by you, the attendees, so we have
> a month to decided on a plan of attack that will make it a productive
> two days. I put together a shared public Google document we can use for
> collecting discussions, and kicked things off with some suggestions
> for work related to the CloudBioLinux project:
>
> https://docs.google.com/document/d/1EFe9YszL5Lp5FjZjJLFhWepsto1jhC6oASWcG4Wlnds/edit?hl=en
>
> Please feel welcome to mention other ideas on the list or in the
> document, and also just say hello and introduce yourselves.
>
> Looking forward to beautiful Vienna,
> Brad
>
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>
>
> --
> If I haven't seen further, it is by standing in the footprints of giants
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