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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:


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$s\n",@b));
if($s=~/ /){$t.=$c[2];$s=$n[int(rand()*4)]}

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 TWiki Site Map Use to...
Main Home of Main web Search Main web Recent changes in the Main web Get notified of changes to the Main web TWiki home where users and groups are located
TWiki Home of TWiki web Search TWiki web Recent changes in the TWiki web Get notified of changes to the TWiki web TWiki documentation, welcome, registration and other starting points
Blog Home of Blog web Search Blog web Recent changes in the Blog web Get notified of changes to the Blog web Weblog. ...edit individual weblog entries directly.
Fall07 Home of Fall07 web Search Fall07 web Recent changes in the Fall07 web Get notified of changes to the Fall07 web Fall 2007 Teaching Wiki ...post projects, assignments, class pages
Fall08 Home of Fall08 web Search Fall08 web Recent changes in the Fall08 web Get notified of changes to the Fall08 web Fall 2008 class wiki. ...post student projects.
Fall09 Home of Fall09 web Search Fall09 web Recent changes in the Fall09 web Get notified of changes to the Fall09 web Fall 2009 class wiki. ...post student projects, assignments & class pages.
Fall10 Home of Fall10 web Search Fall10 web Recent changes in the Fall10 web Get notified of changes to the Fall10 web Fall 2010 ...post class projects and homework assignments
Fall11 Home of Fall11 web Search Fall11 web Recent changes in the Fall11 web Get notified of changes to the Fall11 web Fall 2011 student web ...post Fall 2011 BioE131 class projects and homework assignments.
JBrowse Home of JBrowse web Search JBrowse web Recent changes in the JBrowse web Get notified of changes to the JBrowse web Wiki node for AJAX GBrowse development ...collaborate on next-generation genome browser development
Research Home of Research web Search Research web Recent changes in the Research web Get notified of changes to the Research web Welcome to TWiki... Users, Groups, Offices. ...publish software, results and analysis.
Sandbox Home of Sandbox web Search Sandbox web Recent changes in the Sandbox web Get notified of changes to the Sandbox web Sandbox test area with all features enabled. ...experiment in an unrestricted hands-on web.
Teaching Home of Teaching web Search Teaching web Recent changes in the Teaching web Get notified of changes to the Teaching web Welcome to TWiki... Users, Groups, Offices. ...publish software, results and analysis.
ZaboArt Home of ZaboArt web Search ZaboArt web Recent changes in the ZaboArt web Get notified of changes to the ZaboArt web Zabo Zabo Art Therapy ...collaborate on art therapy projects.
You can use color coding by web for identification and reference. This table is updated automatically based on WebPreferences settings of the individual webs. Contact ihholmes@gmail.com if you need a separate collaboration web for your team. See also AdminTools.
Legend of icons:   Home of web = Go to the home of the web
Search web = Search the web
  Recent changes in the web = See recent changes in the web
Get notified of changes to the web = Subscribe to get notified of changes by e-mail
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Parents: WebHome
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