Ketil and Christian; I'm glad you will be at Codefest; looking forward to meeting both of you and to a productive time.
These all sound like great targets for work during the two days. I'm not much of a Haskell coder -- I do run Xmonad and read 'Learn you a Haskell' -- but do have one small suggestion. A pet project for me has been trying to make the development environment on CloudBioLinux (http://cloudbiolinux.org/) workable for a wide variety of different languages. If you are interested, it would be really helpful to have your thoughts on libraries and utilities that should be installed by default. The goal is that if a Haskell coder fired up a CloudBioLinux instance they would be able to be immediately productive without a lot of tweaking and installs. Looking forward to talking more in Vienna, Brad > Hi, > > Your points are actually rather good, and I'd like to work on it. > Especially since I am currently changing a lot in my libraries and > this could find it's way into a common lib. One problem might be > that I tend to change stuff as I need it, as I am my only user ;-) > > Regarding iteratee/enumerator/iterIO: I am currently using > enumerator to (re-)implement my data sources. Once you wrap your > head around it, one can use them without too many problems. One > problem I have is that it is not quite clear what library would be > the "best" one. I basically chose enumerator because of better > dependencies (iterIO depends on SSL...) and many supporting > packages. > > Gruss, > Christian > > PS: I'll be at alternative splicing, not BOSC -- it's closer to our > work. > > On Thu, 09 Jun 2011 12:20:53 +0200, Ketil Malde wrote: > >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 > > _______________________________________________ > Biohaskell mailing list > Biohaskell@biohaskell.org > http://malde.org/cgi-bin/mailman/listinfo/biohaskell _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
