README.md, up the version, fix dependency definitions

Gemfile

@@ -2,6 +2,7 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem 'bio'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -12,6 +13,5 @@ group :development do
   gem "cucumber", ">= 0"
   gem "jeweler", "~> 1.8.3"
   gem "bundler", ">= 1.0.21"
-  gem "bio", ">= 1.4.2"
   gem "rdoc", "~> 3.12"
 end

README.md

@@ -2,25 +2,45 @@
 
 [![Build Status](https://secure.travis-ci.org/wwood/bioruby-krona.png)](http://travis-ci.org/wwood/bioruby-krona)
 
-Full description goes here
+This biogem is built around [Krona](http://krona.sourceforge.net/), a flashy way of representing hierarchical data.
 
-Note: this software is under active development!
+## Usage
 
-## Installation
+```bio-krona``` is a pretty simple gem, at this stage, and only implements two useful methods. 
+The first, the static method ```Bio::Krona#html``` is to call the krona software itself (specifically, ```ktImportText```) to generate
+the visualisation in HTML form.
+
+```ruby
+require 'bio-krona'
+
+html = Bio::Krona.html({
+      ['Sponge','Amphimedon']=>3,
+      ['Sponge','Calciums']=>4,
+    })
 
-```sh
-    gem install bio-krona
 ```
 
-## Usage
+It takes as input a hash, where the keys are arrays representing the metadata, and the values are the weightings. In the example above, 
+the data has two levels of hierarchy - first Sponge, second Ampphimedon/Calciums.
+
+The second method ```collapse``` implements a pre-processing step that might be of use when the data is overly complex. 
+It collapses the data so that only a limited number of hierarchy levels are accounted for. 
+The weightings are preseverd by adding up the individual abundances.
 
 ```ruby
-    require 'bio-krona'
+Bio::Krona.collapse({
+   ['Sponge','Amphimedon']=>3,
+   ['Sponge','Calciums']=>4,
+}, 1)
+#=> {['Sponge'] => 7}
+``` 
+
+## Installation
+
+```sh
+gem install bio-krona
 ```
 
-The API doc is online. For more code examples see the test files in
-the source tree.
-
 ## Project home page
 
 Information on the source tree, documentation, examples, issues and
@@ -32,10 +52,7 @@ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
 ## Cite
 
-If you use this software, please cite one of
-
-* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
-* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+```bio-krona``` is currently unpublished. However Krona itself is - see http://krona.sourceforge.net
 
 ## Biogems.info
 

VERSION

@@ -1 +1 @@
-0.0.0
+0.0.1