Structural Bioinformatics Libraries In Haskell.

Question

[Burlappsack]

Hello, I am looking for a Haskell based-bioinformatics library for importing pdb files for the purposes of computational biology research. I have checked the BioHaskell website, and haven't found anything. Are you aware of any structural biology libraries, or even open source applications that use Haskell for this purpose? If there isn't one, and you would like to see one created, what features would you like to see implemented? Thanks, Adam

Answer 1

[Neilfws]

To my knowledge, there are no existing structural biology libraries for Haskell; or if there are, they are effectively invisible - which amounts to the same thing.

BioHaskell is a relatively new addition to the Bio* projects family, presumably because interest in the language for bioinformatics is relatively recent. At present it contain libraries only for sequence-based data.

If you were to develop a library, it should presumably have the same functionality as the existing libraries for other languages: e.g. Bio::PDB for BioRuby, Bio::Structure for Bioperl or Bio.PDB (PDF) for BioPython.

However, given the existence of these already-excellent libraries, I would question the wisdom of developing yet another for a little-used language. If you use only Haskell, you need the functionality, you're happy to write it and you think it's worthwhile and useful to others then fine, go ahead. If you want to get your research done quickly, it's better to learn how to use what's already available.

[Yogesh Pandit]

The BioHaskell Blog - http://blog.malde.org/

Answer 2

[mjgajda]

There are few Protein Data Bank parsing modules that appeared on GitHub over the last year. There is for example long-developed hPDB on Hackage, which is mostly tuned for speed and convenient high-level interface.