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add citation, rdoc => md format of README

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wwood committed Dec 1, 2012
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+# bio-tm_hmm
+
+{<img
+src="https://secure.travis-ci.org/wwood/bioruby-tm_hmm.png"
+/>}[http://travis-ci.org/#!/wwood/bioruby-tm_hmm]
+
+A bioruby plugin for running the transmembrane domain predictor TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results.
+
+## Installation
+
+```
+gem install bio-tm_hmm
+```
+
+## Usage
+
+```
+bio-tm_hmm my.fasta
+```
+
+Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
+
+Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that don't (converse is -g). For instance, to filter out all sequences that have less than 2 predicted transmembrane domains:
+
+```
+bio-tm_hmm -f 2 <my.fasta
+```
+
+## Developers
+
+To use the library
+
+```
+require 'bio-tm_hmm'
+```
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+ http://github.com/wwood/bioruby-tm_hmm
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+ If you use this software, please cite:
+
+[Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum](genomebiology.com/2012/13/11/R108)
+
+Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph and Till S Voss
+
+Genome Biology 2012, 13:R108 doi:10.1186/gb-2012-13-11-r108
+
+## Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
+
+## Copyright
+
+Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
+
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-= bio-tm_hmm
-
-{<img
-src="https://secure.travis-ci.org/wwood/bioruby-tm_hmm.png"
-/>}[http://travis-ci.org/#!/wwood/bioruby-tm_hmm]
-
-A bioruby plugin for running TMHMM automatically on multiple sequences in a FASTA file and manipulation of the results
-
-Note: this software is under active development!
-
-== Installation
-
- gem install bio-tm_hmm
-
-== Usage
-
- bio-tm_hmm my.fasta
-
-Where my.fasta is a FASTA file with one or more protein sequences in it. Output will be a description of the transmembrane domains predicted by TMHMM.
-
-Other options include -f for printing out the fasta sequences that have some number of transmembrane domains in them, and ignoring those that done (converse is -g)
-
- bio-tm_hmm -f 2 <my.fasta
-
-== Developers
-
-To use the library
-
- require 'bio-tm_hmm'
-
-The API doc is online. For more code examples see also the test files in
-the source tree.
-
-== Project home page
-
-Information on the source tree, documentation, issues and how to contribute, see
-
- http://github.com/wwood/bioruby-tm_hmm
-
-The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
-
-== Cite
-
- If you use this software, please cite one of
-
-* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
-* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
-
-== Biogems.info
-
-This Biogem is published at http://biogems.info/index.html#bio-tm_hmm
-
-== Copyright
-
-Copyright (c) 2012 Ben J Woodcroft. See LICENSE.txt for further details.
-

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