Bio Wiki

About Biowiki.org

biowiki.org is a lab notebook for the Holmes lab at the University of California, Berkeley.

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 [/search/Main/?search=Wikipedia: 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, RNAAlignmentViewers...)
• 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 ADebian Box...)
• links to compbio resources (Compbio Conferences, Open Bio Projects...)
• topic-specific bibliographies (Transposon Papers, Phylogenetic Alignment Reader, Nucleic Acid Engineering...)
• bioinformatics analysis project pages (Fly Nc Rna, Twelve Fly Screen, Rna Models...)
• teaching pages (Cryptanalysis Exercises, Unix Tutorial...)
• 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)

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

Here is a wordle.net tag cloud:

Using this wiki

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

• TWiki.WelcomeGuest: Look here first to get you rolling on TWiki.
• TWiki.TWikiSite: Explains what TWiki (the software running this website) is all about.
• TWiki.TWikiRegistration: Create your account in order to edit topics.
• Documentation:
  • TWiki.TWikiFAQ has a list of frequently asked questions.
  • TWiki.TWikiDocumentation is the implementation documentation of TWiki.
  • TWiki.TWikiHistory shows TWiki's implementation history.
• How to edit text:
  • TWiki.GoodStyle: Things to consider when changing text.
  • TWiki.TextFormattingRules: Easy to learn rules for editing text.
  • TWiki.TextFormattingFAQ: Answers to frequently asked questions about text formatting.
• TWiki.: TWiki site-level preferences

TWiki.WebSiteTools

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 Web Critic).

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:

• TWiki.EFetchPlugin for inline PubMed citations
• TWiki.MathModePlugin for inline latex expansions $(\kappa\epsilon\omega\ell\ !)$
• TWiki.SessionPlugin for authentication
• TWiki.TouchGraphPlugin for the 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.WebHome at Web Home.)

TWiki.SiteMap