Hi Ketil, submit as a Haskell GSoC! I'd be very interested in hearing about multitape applications for DP. And I think I could help with performance issues. Once PloS ONE is back, I'll take a look at your paper.
Gruss, Christian PS: now that I have handed in my thesis, I should have time to publish the multitrack extensions to ADPfusion, might be possible to draw some pointers from that for your stuff / gsoc. * Ketil Malde <ke...@malde.org> [03.04.2013 22:40]: > > [CC everybody including the biohaskell list. Let me know if any of you > want off. :-) ] > > Pjotr Prins <pjotr2...@thebird.nl> writes: > > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > > For Biopython (3x), BioRuby (5x) and BioJava (4x) I found project ideas. > > > The others are missing. > > > There is still a (rather small) window of opportunity for adding > > ideas. > > I have one thing that might work well as a SOC project, if the right > student could be found. > > Basically, I and a colleague recently developed and published a method > and implementation for more sensitive pairwise alignments. The paper is > here, I think (PLoS ONE seems to be down atm): > http://dx.plos.org/10.1371/journal.pone.0054422 > > I'm really happy about the results, if nothing else, check the SCOP > benchmark. Although it's difficult to construct a good test case using > more complex methods (training sets for HMMs and whatnot) I don't know > anything that is as good as this. We're using it for annotation of > genes. > > The current implementation is in Haskell, and although it works > correctly, it is a bit slow, and more problematic, it consumes too much > memory (so going multi-threaded, although pretty easy, won't be of any > help). > > I would like to make this into a less resource intensive (and thus more > practical) tool, and there are two ways I can think of to go about this: > > 1) Optimize the Haskell program > > 2) Reimplement the algorithm (or parts of it) in a different language > > Advantages of 1: > > * Already have a working program, and the type system makes it easy to > refactor without introducing errors. > * Haskell supports lots of good multi-threading programming models (like > STM) > * I know Haskell pretty well, and will be hopefully be able to mentor. > > Disadvantages: > > * Haskell has some good debugging tools, but they tend to work really > poorly for large memory (i.e. it takes a long time to generate > profiles) > * Needs somebody with a bit (or a lot) of experience optimizing Haskell, > and good knowledge of high-perf libraries (like vector) > > Advantages of 2: > > * Easier to get a student with adequate skills. > * More predictable performance models in other languages. > * Easier to compile and install for many users. > > Disadvantages: > > * Ideally, should know enough Haskell to read and understand the code. > * Likely needs a co-mentor with knowledge of the language in question. > > Is this something I could or should submit as a task? > > -k > -- > If I haven't seen further, it is by standing in the footprints of giants > _______________________________________________ > Biohaskell mailing list > Biohaskell@biohaskell.org > http://malde.org/cgi-bin/mailman/listinfo/biohaskell
pgpxqVdccgpTe.pgp
Description: PGP signature
_______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
