Okay, a rough draft below, hope you can deal with the LaTeX markup.
Please read through it and comment. Especially if anybody feels left
out, speak up - this is put together in a hurry, so any slight is higly
unintentional. Also, suggest links, or other info that should be
included.
% Biohaskell-KB.tex
\begin{hcarentry}[updated]{Biohaskell}
\label{bioinformatics}
\report{Ketil Malde}%05/11
\participants{Christian H\"oner zu Siederdissen, Nick Ignolia, Felipe Almeida Lessa}
\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 sports several libraries and
applications. The
\href{http://biohaskell.org}{biohaskell web site} collects
information about
Anybody interested in the combination of Haskell and bioinformatics is encouraged
to sign up to the
\href{http://biohaskell.org/cgi-bin/mailman/listinfo/biohaskell}{mailing list}.
Bioinformatics is a diverse field, and consequently, we have
different \href{http://biohaskell.org/Libraries}{libraries} covering mostly-separate areas.
This summer, some of us participated at the
\href{http://www.open-bio.org/wiki/Codefest_2011}{BOSC codefest}, and
we agreed to factor out common data types that other libraries could
use. The result is
\href{http://hackage.haskell.org/packages/biocore}{biocore}, currently
in revision 0.2. There is an ongoing effort to adapt existing
libraries to biocore.
% Libraries
The \href{http://biohaskell.org/Libraries/Bio}{\emph{biolib library}}
that supports various sequence and alignment-oriented file formats and
operations, is now in the process of being obsoleted. Functionality
is gradually being factored out, and this has so far resulted in
separate libraries for 454 sequencing reads (biosff), and PSL
alignment files (biopsl).
\href{http://biohaskell.org/Libraries/Biobase}{Biobase} library supports
secondary structure prediction of single RNA molecules (a Haskell port
of the Vienna RNAfold program, a polynomial-time version of the
MC-fold pipeline, and a novel algorithm, RNAwolf, for extended
secondary structure prediction). This includes the ability to work
with different file formats, representing canonical RNA structures and
non-canonical extensions.
The \href{http://hackage.haskell.org/package/biostockholm}{biostockholm}
package supports parsing and pretty printing of files in Stockholm 1.0
format. These formats are used by \href{http://pfam.sanger.ac.uk/}{Pfam}
and \href{http://rfam.sanger.ac.uk/}{Rfam} for multiple sequence alignments.
Finally, there is
\href{http://www.ingolia-lab.org/software/samtools/}{samtools} wrapping the samtools C library for accessing and
manipulating BAM alignment files, and
\href{http://hackage.haskell.org/package/seqloc}{seqloc} providing functionality for manipulating sequence
locations and annotation.
% Applications?
% Papers?
\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
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