FWIW, I sent the attached in as a revised entry, after some modification
from Michal. Feel free to modify/add/update as you see fit.
% Biohaskell-KB.tex
\begin{hcarentry}[updated]{Biohaskell}
\label{bioinformatics}
\report{Ketil Malde, Michal J.\ Gajda}%11/13
\participants{Christian H\"oner zu Siederdissen, Nick Ignolia, Felipe
Almeida Lessa, Dan Fornika, Maik Riechert, Ashish Agarwal, Grant Rotskoff}
\makeheader
%**<img width=200 src="./biohaskell.svg">
%*ignore
\begin{center}
\includegraphics[width=0.235\textwidth]{html/biohaskell.pdf}
\end{center}
%*endignore
Bioinformatics in Haskell is a steadily growing field, and the
\href{http://hackage.haskell.org/packages/archive/pkg-list.html#cat:bioinformatics}{\emph{Bio}
section} on Hackage now contains 53 libraries and applications. The
\href{http://biohaskell.org}{biohaskell web site} coordinates this
effort, and provides documentation and related information.
Anybody interested in the combination of Haskell and bioinformatics is
encouraged
to sign up to the mailing list (currently by emailing
\href{mailto:ke...@malde.org}{Ketil}), and to register and document their
contributions on the
\href{http://biohaskell.org}{http://biohaskell.org} wiki.
BioHaskell now contains a fledgling collection of libraries for
structural analysis of biomolecules. \texttt{hPDB} is a parallel parser of
Protein DataBank file format, which parses the largest structures faster than
single-threaded Python code, and faster than parallel BioJava parser. It
uses an octree data structure for fast querying of atom positions and
contacts, and Iterable class to allow for iteration over deeply contained
objects within hierarchical collections. The author of the library, Michal J.\
Gajda plans to soon release other
libraries for processing biomolecular data, in particular \texttt{parseSTAR}
for parsing STAR* format used for BMRB database of nuclear magnetic resonance
data, and \texttt{hDat} library for processing small-angle scattering data.
\FurtherReading
\begin{compactitem}
\item \url{http://biohaskell.org}
\item \url{http://blog.malde.org}
\item \url{http://hackage.haskell.org/package/hPDB}
\item \url{http://hackage.haskell.org/package/Octree}
\item \url{http://hackage.haskell.org/package/Iterable}
\item \url{http://www.tbi.univie.ac.at/~choener/haskell/}
\item \url{http://adp-multi.ruhoh.com}
\end{compactitem}
\end{hcarentry}
Christian Höner zu Siederdissen <choe...@tbi.univie.ac.at> writes:
> Hi Ketil,
>
> the Biohaskell part could remain as is, I think. I'll take a closer look
> tonight (I need to go over two other sections as well).
>
> Viele Gruesse,
> Christian
>
> * Ketil Malde <ke...@malde.org> [11.11.2013 05:34]:
>>
>> Hi, all
>>
>> I just got the HCAR draft report in my inbox, and suddenly realized I'd
>> forgotten all about it. The text is therefore the same as last
>> time. It's fairly general, with links etc. Does anybody object strongly
>> to just letting it stay that way? If anybody wants to change something,
>> it's still possible to do so, but we need to act quickly.
>>
>> -k
>> --
>> If I haven't seen further, it is by standing in the footprints of giants
--
If I haven't seen further, it is by standing in the footprints of giants
