* Ketil Malde <ke...@malde.org> [01.11.2011 09:53]: > 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?
Just keep it as is. I can use the Biobse wiki page for the overview!
>
> > 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?)
I only put them in there because of the % publications note. The other
reports are without publications, we should follow that...
Gruss,
Christian
>
> % 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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