Christian Höner zu Siederdissen <choe...@tbi.univie.ac.at> writes:
Thanks for the reply, I've tried to address the issues raised (included
below). I'm not clear on how/if you want links from the Biobase*
paragraph, any thoughts?
> note, do we want to give papers? If yes, here are the three most fitting
> ones. The top-most is a bit theoretical, though ;-)
Perhaps we could make a wiki page listing publications? I don't think
we'll include it in the HCAR report (are other contributors doing it?)
% 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} 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
\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 deprecated. 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}{Biobase*}
The Biobase-prefixed libraries provide basic functionality for a
number of data formats. A number of additional libraries are provided:
RNAfold is a partial port the ViennaRNA package, MC-Fold-DP: a
polynomial-time version of the original MC-Fold pipeline, while
RNAwolf provides a novel RNA-folding algorithm with non-canonical
secondary structures. On the level of non-coding RNA prediction,
CMCompare is used to assess the discriminatory power of RNA family
models.
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.html}
\end{compactitem}
\end{hcarentry}
-k
--
If I haven't seen further, it is by standing in the footprints of giants
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