Hi,
It's that time of year again... Janis V wants our contricution to the
HCAR communities and activities report, and I have made the following
draft. Please take a look, and report back with any inaccuracies,
undesirabilities, or missing pieces. Deadline for submission is May 1,
so any feedback ASAP, please.
% Biohaskell-KB.tex
\begin{hcarentry}[updated]{Biohaskell}
\label{bioinformatics}
\report{Ketil Malde}
\participants{Christian H\"oner zu Siederdissen, Nick Ignolia}%11/10
\makeheader
%**<img width=400 src="./bg2-bh.jpg">
%*ignore
\begin{center}
\includegraphics[width=0.235\textwidth]{html/bg2-bh.jpg}
\end{center}
%*endignore
Bioinformatics in Haskell is a steadily growing field, and the
relevant section on Hackage now sports several libraries and
applications. In the past year, we have started to accumulate
information related to biohaskell on the
\href{http://biohaskell.org}{biohaskell web site} and encourage anyone
interested to contribute, and also to sign up to the
\href{http://biohaskell.org/cgi-bin/mailman/listinfo/biohaskell}{mailing list}.
There now exists several
\href{http://biohaskell.org/Libraries}{libraries} for bioinformatics
in Haskell, each covering different aspects of the field.
These includes the
\href{http://biohaskell.org/Libraries/Bio}{\emph{biolib library}}
supporting various sequence and alignment-oriented file formats and operations,
\href{http://hackage.haskell.org/package/seqloc}{seqloc} providing
functionality for manipulating sequence
locations and annotation,
\href{http://biohaskell.org/Libraries/Biobase}{Biobase}
% and \href{}{RNAfold}?
for working with RNA secondary structure, and
\href{http://www.ingolia-lab.org/software/samtools/}{samtools} wrapping the
samtools C library for accessing and
manipulating BAM alignment files.
\FurtherReading
\begin{compactitem}
\item \url{http://biohaskell.org}
\item \url{http://blog.malde.org/}
\item \url{http://www.tbi.univie.ac.at/~choener/Haskell/}
\end{compactitem}
\end{hcarentry}
-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
