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:
- Holmes lab research output (PaperArchive, FreeSoftware, PhyloFilm...)
- software documentation pages (DART, GffTools, StockholmTools, BubblePlots, RNAAlignmentViewers...)
- file formats (StockholmFormat, XrateFormat, GffFormat, FastaFormat, NewickFormat, CigarFormat...)
- essays on algorithms and applications (StringTransducers, StochasticGrammars, PhyloAlignment...)
- tutorials for software developed here (StemlocTutorial, MercatorPerl, JBrowse tutorial...)
- tutorials for third-party software (HowToUseSunGridEngine, HowToAdministerSunGridEngine, HowToSetUpADebianBox...)
- links to compbio resources (CompbioConferences, OpenBioProjects...)
- topic-specific bibliographies (TransposonPapers, PhylogeneticAlignmentReader, NucleicAcidEngineering...)
- bioinformatics analysis project pages (FlyNcRna, TwelveFlyScreen, RnaModels...)
- teaching pages (BioE131, BioE241, CryptanalysisExercises, InformationContentOfDNA, UnixTutorial...)
- student project pages (Bullard Galluser Hansen, van Belle, Sriram, more...)
- user pages (IanHolmes, AndrewUzilov, RobertBradley...)
- documentation of Holmes lab setup (Installing CentOS On Cluster, Mounting NFS Through SSH Tunnel, TSM Backup System, DjbDns...)
- idle & opinionated rants (Why Dart is not in Java, Ian defends XP, Why MCMC is Networking for Modelers, BioinformaticsWorkflows...)
- more carefully-reasoned opinion pieces (GenomeWiki, MakefileManifesto)
- blog entries (AdaLovelaceDay, WikisForSpooks, WarGamesAndHoneyBees, SwearAtTheMachine...)
This is an incomplete list; pretty much anything goes...
Here, for example, is our wordle.net tag cloud
as of 8/25/2008:
Using this wiki
Here are some useful links about this wiki site, how to navigate & participate in it.
- WelcomeGuest: Look here first to get you rolling on Biowiki.
- TWikiSite: Explains what TWiki (the software running this website) is all about.
- TWikiRegistration: Create your account in order to edit topics.
- How to edit text:
- TWikiPreferences: Biowiki site-level preferences
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
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
(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
This site runs TWiki
software with the following plugins:
The Biowiki logo was generated using figlet
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];
Below is a site map and a set of useful links.
(This preserves the default content usually provided by TWiki
|| Search the web
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Biowiki content is in the public domain.
Comments on this site? BioWiki