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analysis
config
data
helpers
model
spec
vendor/gems
www
.gitignore
README
Rakefile

README

This a set of bioinformatics experiments as well as a dynamic webpage to display the results

## model

This directory contains a set of datamapper classes that allow rows in the database to be manipulated as simple ruby objects.

 * project.rb Main class that describes the entire project
 * gene.rb Holds sequence data about yeast genes

## config

Contains general ruby configuration data, as well as ramaze configuration

* environment.rb Requires necessary ruby gems. Loads databases parameters. Loads classes and controllers.
* database.yml Database access parameters. In YAML format. Should be created for each installation of this code.
* config,yml General project configuration parameters. Ramaze port, server, and rendering engine. Should also be configured for each installation.

## controller

Ramaze controllers that serve up data to views

## view

HTML generators for www front

## spec

Data testing classes using rspec

## analysis

Rake files and data that run the bioinformatics analysis. Organised by linear running order, ie 002 should only depend on data from 001, and nothing from 003.

## start.rb

Starts the ramaze web server
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