[Haskell-cafe] [ANNOUNCE]hPDB - Is it the fastest parallel PDB parser? Part of structural bioinformatics library collection...

Michal J Gajda mgajda at mimuw.edu.pl
Sun Nov 24 23:18:16 UTC 2013

Dear Haskellers,

I would like to present a benchmark of Protein Databank parsers that
indicates that one written in Haskell seems to outpace all others when
using 4 or more of parallel cores:

hPDB - Haskell library for processing atomic biomolecular structures in
Protein Data Bank format -- Michal Jan Gajda
BMC Research Notes.2013, 6:483.
DOI: 10.1186/1756-0500-6-483
URL: http://www.biomedcentral.com/1756-0500/6/483

Please let me know if you know of any other parsers that could be added to
this benchmark.

Along with hTalos, and parseSTAR parser libraries for nuclear magnetic
resonance data it adds to growing collection of bioinformatic libraries
written in Haskell.

Together with CloudHaskell and modern 48-core machines, they allow to
process multigigabyte bioinformatic databases in a matter of few minutes
(slightly over 8 minutes in case of over 10GB of PDB.)

If interested, please see: http://biohaskell.org/.
  Best regards
    Michał J. Gajda
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