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Links
misc bio links
Open bio projects
Bio wikis, blogs
Meetings, journals
off-site links
Rfam / Pfam
GMOD/GBrowse
UCSC, Ensembl
Bioperl wiki
AAA fly wiki
ISCB; RNA society


journals
Nature, Science
Cell, PLoS Biol
Nature Genetics
Genome Research
Genome Biology
PLoS Comp Bio
NAR, Mol Biol Evol
J Comp Biol
BMC Bioinformatics
Bioinformatics
Phys Rev Lett


bioinformatics blogs
fungalgenomes.org
Jason Stajich
Buried Treasure
Cyrus Harmon
Flags and Lollipops
nodalpoint.org
mutantphenotype
Yi Xing
Yokofakun
Propeller Twist
Notes from the Biomass
bioinformatics.org
Biohackery
Andrew Dalke
Neil Saunders
Personal Genome
iSpecies blog
bioinformaticsblog
Public Rambling
Inforbiomatica
hublog
Oakleys corner


bio/science blogs
Biocurious
Declan Butler
Nascent
Pharyngula
Bioethics.net
Free Association
young female scientist
OpenScience project
genetics+health
evolgen
post-genomics
gene expression
Informaticopia
Biopeer
Tangled Bank
Cavalcade of Mammals
Triplepoint
three-toed sloth
panda's thumb
stranger fruit
Genetic Chaos
In the Pipeline


tech blogs
everybody :-x esr
xkcd
27B/6
geekdad
Bruce Schneier
videogameworkout
Annalee Newitz
Rudy Rucker
Bruce Sterling
Need To Know
The Register
The Scientist
Raph Koster
jay is games
Red Orbit
+ve tech journal
Laughing Meme
Respectful Insolence
Braintickle


collaborators
Alex Bateman
Casey Bergman
Ewan Birney
Rachel Brem
Steven Brenner
Bill Bruno
Sue Celniker
Richard Durbin
Sean Eddy
Mike Eisen
Nick Goldman
Richard Goldstein
Andreas Heger
Jotun Hein
Steve Holbrook
Andrew Holmes
John Huelsenbeck
Marcin Joachimiak
Sam Griffiths Jones
Suzi Lewis
Gerton Lunter
Chris Mungall
Janet Newman
Rasmus Nielsen
Lior Pachter
Tom Peat
Chris Ponting
David Schaffer
Kimmen Sjolander
Guy Slater
Jason Stajich
Lincoln Stein


PageRank Checker

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 Paper Archive here, and a collection of Free Software 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 String Transducers), the promotion of specific algorithmic ideas (e.g. Phylo Alignment), 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).

Specifically, types of page to be found here include:

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

Other biowikis

From an early stage we have also tried to collect links to other Bio Wikis, and we continue to do so. More recently we've started collecting links to Bio Blogs (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 Bio Wikis 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) than 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:

Twiki stuff

Below is a site map and a set of useful links for editing the wiki. (This preserves the default content usually provided by TWiki at Web Home.)

The Biowiki logo was generated using figlet.

Web Biowiki 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 Welcome to Biowiki... Users, Groups, Offices. ...publish software, results and analysis.
TWiki Home of TWiki web Search TWiki web Recent changes in the TWiki web Get notified of changes to the TWiki web Welcome, Registration, and other StartingPoints; TWiki history & Wiki style; All the docs... ...discover TWiki details, and how to start your own site.
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
GBrowse Home of GBrowse web Search GBrowse web Recent changes in the GBrowse web Get notified of changes to the GBrowse 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 Biowiki... 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 Biowiki... Users, Groups?, Offices. ...publish software, results and analysis.
Trash Home of Trash web Search Trash web Recent changes in the Trash web Get notified of changes to the Trash web? Welcome to Biowiki... Users, Groups, Offices?. ...publish software, results and analysis.
Zabo Art 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 ihh@fruitfly.org 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

Biowiki.Main Web:

Biowiki.TWiki Web:

Notes:

  • You are currently in the Main web. The color code for this web is this background, so you know where you are.
  • If you are not familiar with the Biowiki collaboration platform, please visit WelcomeGuest first.
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