[BioRuby] BioRuby interesting links and documentation.

[Michael Barton]

I thought I should reply to Raoul's email with a different topic name.

One way could be to share interesting links through some sort of feed?
A community blog or twitter? I think the wiki needs some attention in places,
e.g. the sample codes page has many headings with "TBD" as the content.

The doc rails project seems to have been quite successful for the Rails
community. Rather than a wiki it's a static site on github. I think the reason
of it's success is that one person is responsible for it (@pratiknaik).

On Tue, Feb 22, 2011 at 07:36:36PM +0100, Raoul Bonnal wrote:
> Hi Michael, thanks for the post. Why not open a Geek section on the wiki for
> this type of links ? _____  
> 
> From: Michael Barton [mailto:mail at michaelbarton.me.uk] To: BioRuby Mailing
> List [mailto:bioruby at lists.open-bio.org] Sent: Tue, 22 Feb 2011 17:48:21
> +0100 Subject: Re: [BioRuby] FFI to Smith/Waterman and Needleman/Wunsh
> C-extension
> 
> Thank you Naohisa and Francesco for your suggestions. I will try
> experimenting with these two libraries. I had also just read an interesting
> article on using C extensions in Ruby which I thought might be of general
> interest to the mailing list -
>   
>   http://robots.thoughtbot.com/post/1037240922
>   
>   On Tue, Feb 22, 2011 at 06:11:20PM +0900, Naohisa GOTO wrote:
>   > Hi,
>   > 
>   > There was SWlib, an implementation of Smith-Waterman algorithm for Ruby.
>   > It was written by OKUJI K. Yoshinori in 2001. Since it is very old, some
>   > modification would be needed for correct working.
>   > http://bioruby.open-bio.org/contrib/swlib/
>   > 
>   > Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>   > 
>   > On Mon, 21 Feb 2011 12:06:07 -0500 Michael Barton
>   > <mail at michaelbarton.me.uk> wrote:
>   > 
>   > > Hi,
>   > > 
>   > > Does anyone know of a ruby library for doing local and global sequence
>   > > alignment? I'm interested in performing these kind of alignments in
>   > > ruby but would prefer not to call command line tools such as EMBOSS.
>   > > I think it could be useful to have a ruby gem which installs
>   > > a C-extension for allowing for reasonably fast alignment. A cursory
>   > > look on pubmed turned these links for C libraries.
>   > > 
>   > > http://www.ncbi.nlm.nih.gov/pubmed/18959793
>   > > http://www.ncbi.nlm.nih.gov/books/NBK7151/
>   > > 
>   > > Mike
>   > 
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>