Hi, always good to have another haskell user in bioinformatics.
Concerning your question you are both, lucky and unlucky ;-) There is no single unified "biohaskell" library but rather a collection of different things. On hackage, you find libraries and programs by Ketil (mainly bio and dependent stuff) and me (Biobase and dependent stuff). I think, this is mostly because there are not enough people working on the same problem that would warrant deeper cooperation. For me it is like this: - I am a user of Ketils bio lib and (obviously) a user of my own Biobase. - should we at some point need to work on s.th. together, it will likely be easy My suggestion is to just give the thing a name (eg. polyphred-xml) and push it to hackage. Use whatever dependencies you like. Then you are set and others can use it or take a look. Btw. should we, as a group, at some point decide that incorporating everything into a "big library", that would work for me. But the approach of having smaller libraries that can be easily stitched together seems to work quite well for me. Btw. you might want to consider attending BOSC 2011 and the Hackathon this year in Vienna. Both Ketil and me (and people from other projects like bioperl) are there (I think ;-). Gruss, Christian PS: My approach to library dependencies is to use the library that makes my life easier, completely ignoring the consequences. Using cabal-dev that works quite well. * Dan Fornika <dforn...@gmail.com> [04.03.2011 20:15]: > Hi, > > My name is Dan Fornika, I'm a genetics grad student in Canada and > beginning self-taught haskell programmer. I'm making some progress on a > parser for Polyphred XML output (based on HXT). > > I started the project with the intention of contributing it to > BioHaskell, and I'd like to ask about how I can do this. I've never > contributed to an open-source project before. > > I noticed that there are other XML parsers based on other Haskell > modules (tagsoup). Will my choice of XML library prevent it from being > incorporated into the project? It looks like HXT is the most > full-featured and well-supported XML handling library right now, but it > is a 'bigger' dependency than tagsoup. > > I'm sure my code is pretty fragile and verbose, but I don't know what > the best way is to get some more experienced eyeballs to look at it. > Should I just attach it to a message and send it to the list? > > Apologies for my somewhat vague description, I'm learning as fast as I can! > > Dan > > P.S. I've been trying to get an account for the wiki but I've been > getting error messages: > > Server error: : commitAndReleaseBuffer: hardware fault (Input/output error) > _______________________________________________ > Biohaskell mailing list > Biohaskell@biohaskell.org > http://malde.org/cgi-bin/mailman/listinfo/biohaskell
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