Hi,
l.19 is there something missing?
l.25 mostly-separate -> mostly separate
l.38 being obsoleted -> being deprecated
l.43++ {Biobase} library -> {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.
l.70 http://www.tbi.univie.ac.at/~choener/haskell.htmlnote, I have to change the biohaskell webpage, as now biobase is deprecated, 'my' library split is mostly complete note, I have rewritten the whole library part for Biobase* and descendents. I am not quite sure about "applications" as I basically want to provide everything as a library and have only small wrappers for shell-based programming. note, do we want to give papers? If yes, here are the three most fitting ones. The top-most is a bit theoretical, though ;-) Giegerich, Robert, and Christian Höner zu Siederdissen. 2011. Semantics and Ambiguity of Stochastic RNA Family Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8: 499–516. doi:10.1109/TCBB.2010.12. Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011. A Folding Algorithm for Extended RNA Secondary Structures. Bioinformatics 27: 129–36. doi:10.1093/bioinformatics/btr220. Höner zu Siederdissen, Christian, and Ivo L. Hofacker. 2010. Discriminatory power of RNA family models. Bioinformatics 26: 453–59. doi:10.1093/bioinformatics/btq370. Gruss, Christian * Ketil Malde <[email protected]> [31.10.2011 11:26]: > > 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 > _______________________________________________ > Biohaskell mailing list > [email protected] > http://malde.org/cgi-bin/mailman/listinfo/biohaskell
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