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Biowiki . Main . BioWiki

Biowiki . Main . BioWiki

About Biowiki.org

biowiki.org is a server hosting various wikis, including

Content of this site

Mostly, this site is a repository of ideas and content for the Holmes lab. For example, you can find our PaperArchive here, and a collection of FreeSoftware for evolutionary probabilistic bioinformatics.

Please note that this site is NOT trying to be wikipedia. Wikipedia requires consensus, encourages a neutral point of view and prohibits original research. For certain applications in bioinformatics, this works well; e.g. the collaboration between Rfam and Wikipedia to create wikipedia pages for ncRNA gene families. For other applications, the rules may be too restrictive; e.g. the collaborative development of theoretical frameworks (such as StringTransducers), the promotion of specific algorithmic ideas (e.g. PhyloAlignment), or the maintenance of project-specific webpages (e.g. DART or the Holmes lab's xrate pipeline). These latter pages are the sort of thing to be cultivated on biowiki.org (though we do also have many links to wikipedia).

Nor is this a GenomeWiki, a GeneWiki or any of various other types of bioinformatics-wiki (though we do like to discuss such things here; see e.g. the pages linked in this paragraph).

Specifically, types of page to be found here include:

This is an incomplete list; pretty much anything goes...

Here, for example, is our wordle.net tag cloud as of 8/25/2008:

Biowiki.org tag cloud from wordle.net

Using this wiki

Here are some useful links about this wiki site, how to navigate & participate in it.

Other "biowiki"s

From an early stage we have also tried to collect links to other BioWikis, and we continue to do so. More recently we've started collecting links to BioBlogs (see also the list on the left) and doing some vaguely bloglike stuff ourselves (e.g. see WebCritic).

Several other sites call themselves "biowiki" (hey, it's a great idea). For example, this one (commercially curated by Oxford Informatics Ltd) and this one (Jong Park's site). We maintain a list of links to all of these at the top of the BioWikis page. Most of these are apparently trying to be an encyclopaedic/impartial collection of links, i.e. something like Wikipedia; in contrast, biowiki.org unabashedly promotes our views on bioinformatics software and algorithms. We are, perhaps, philosophically closer to Ward Cunningham's original wiki at c2.com (the first ever wiki, intended for spirited discussion of software design patterns) than we are to wikipedia.

Quite obviously, there are things to be said for all those different approaches. A wiki is really just a particular kind of social web application, and we long ago gave up trying to be jealous about the concept, which (after all) we stole from Ward in the first place wink

Server software

This site runs TWiki software with the following plugins:

Trivia

The Biowiki logo was generated using figlet and this:

perl -e '@n=qw(a c g t);@c=map(chr(27)."[".$_."m",30..37);
@b=`figlet -f roman BioWiki`;grep(chomp,@b);$l=$b[@b-1];
unshift@b,$l,$l,$l;$s=" "x20;$b=join("",map("$s$_$s$s$s\n",@b));
$c="";for($i=0;$i<length$b;++$i){$s=substr($b,$i,1);
if($s=~/ /){$t.=$c[2];$s=$n[int(rand()*4)]}
else{$t.=$c[7]}$t.=$s}print$t'

Site map

Below is a site map and a set of useful links. (This preserves the default content usually provided by TWiki at WebHome.)

Web Description Links
Main
Welcome to Biowiki... Users, Groups, Offices.
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TWiki
TWiki documentation, welcome guest and user registration
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Blog
Weblog.
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Fall07
Fall 2007 Teaching Wiki
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Fall08
Fall 2008 class wiki.
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Fall09
Fall 2009 class wiki.
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Fall10
Fall 2010
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Fall11
Fall 2011 student web
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JBrowse
Wiki node for AJAX GBrowse development
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Research
Welcome to Biowiki... Users, Groups, Offices.
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Sandbox
Sandbox test area with all features enabled.
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Teaching
Welcome to Biowiki... Users, Groups, Offices.
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ZaboArt
Zabo Zabo Art Therapy
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TIP Webs are color-coded for identification and reference. Contact wikigardener@postbox.biowiki.org if you need a workspace web for your team.

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----- Revision r144 - 2009-04-30 - 03:23:40 - IanHolmes
Biowiki content is in the public domain.
Comments on this site? BioWiki">Send feedback