About Biowiki.org

biowiki.org is a server hosting various wikis, including

• A lab notebook for the Holmes lab at the University of California, Berkeley;
• A weblog for the Holmes lab;
• A developers' wiki for JBrowse, the AJAX interface to the generic genome browser;
• A teaching wiki for classes in the Department of Bioengineering at UC Berkeley.

• About Biowiki.org
  • Content of this site
  • Using this wiki
  • Other "biowiki"s
  • Server software
    • Trivia
  • Site map

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).

Nor is this a Genome Wiki, a Gene Wiki 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 (Paper Archive, Free Software, Phylo Film...)
• software documentation pages (DART, Gff Tools, Stockholm Tools, Bubble Plots, RNA Alignment Viewers...)
• file formats (Stockholm Format, Xrate Format, Gff Format, Fasta Format, Newick Format, Cigar Format...)
• essays on algorithms and applications (String Transducers, Stochastic Grammars, Phylo Alignment...)
• tutorials for software developed here (Stemloc Tutorial, Mercator Perl, JBrowse tutorial...)
• tutorials for third-party software (How To Use Sun Grid Engine, How To Administer Sun Grid Engine, How To Set Up A Debian Box...)
• links to compbio resources (Compbio Conferences, Open Bio Projects...)
• topic-specific bibliographies (Transposon Papers, Phylogenetic Alignment Reader, NucleicAcidEngineering...)
• bioinformatics analysis project pages (Fly Nc Rna, Twelve Fly Screen, Rna Models...)
• teaching pages (BioE131, BioE241, CryptanalysisExercises, InformationContentOfDNA, UnixTutorial...)
• student project pages (Bullard Galluser Hansen, van Belle, Sriram, more...)
• user pages (Ian Holmes, Andrew Uzilov, Robert Bradley...)
• documentation of Holmes lab setup (Installing CentOS On Cluster, Mounting NFS Through SSH Tunnel, TSM Backup System, Djb Dns...)
• idle & opinionated rants (Why Dart is not in Java, Ian defends XP, Why MCMC is Networking for Modelers, Bioinformatics Workflows...)
• more carefully-reasoned opinion pieces (Genome Wiki, Makefile Manifesto)
• blog entries (AdaLovelaceDay, WikisForSpooks, WarGamesAndHoneyBees, SwearAtTheMachine...)

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.
• Documentation:
  • TWikiFAQ has a list of frequently asked questions.
  • TWikiDocumentation is the implementation documentation of TWiki.
  • TWikiHistory shows TWiki's implementation history.
• How to edit text:
  • GoodStyle: Things to consider when changing text.
  • TextFormattingRules: Easy to learn rules for editing text.
  • TextFormattingFAQ: Answers to frequently asked questions about text formatting.
• TWikiPreferences: Biowiki site-level preferences

Other "biowiki"s

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, 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

Server software

This site runs TWiki software with the following plugins:

• EFetchPlugin for inline PubMed citations
• MathModePlugin for inline latex expansions
• SessionPlugin for authentication
• TouchGraphPlugin for the Graph applet
• Various other local enhancements

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 Web Home.)

Web	Biowiki Site Map	Use to...
Main	Welcome to Biowiki... Users, Groups, Offices.	...publish software, results and analysis.
TWiki	Welcome, Registration, and other StartingPoints; TWiki history & Wiki style; All the docs...	...discover TWiki details, and how to start your own site.
Blog	Weblog.	...edit individual weblog entries directly.
Fall07   ?	Fall 2007 Teaching Wiki	...post projects, assignments, class pages
Fall08	Fall 2008 class wiki.	...post student projects.
JBrowse	Wiki node for AJAX GBrowse development	...collaborate on next-generation genome browser development
Research	Welcome to Biowiki... Users?, Groups?, Offices?.	...publish software, results and analysis.
Sandbox	Sandbox test area with all features enabled.	...experiment in an unrestricted hands-on web.
Teaching	Welcome to Biowiki... Users, Groups?, Offices.	...publish software, results and analysis.
Zabo Art	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 wikigardener@postbox.biowiki.org if you need a separate collaboration web for your team. See also AdminTools.

Legend of icons:

= Go to the home of the web = Search the web

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