SLIMarray¶ ↑

What is it?¶ ↑

SLIMarray is a sample tracking system for microarrays. It is geared primarily towards a “Core Facility” model, where end users submit samples to a core facility and then the core takes care of actually running the samples on the microarray instruments. SLIMarray captures meta data about samples as they are submitted, and then lets the core facility track the samples through being run on a hybridized, and having raw data generated. Much of the sample information is available through a REST-like API.

How do I install it?¶ ↑

SLIMarray can be installed either as a standalone application, or using shared infrastructure that allows single sign-on and shared users and lab groups with other applications such as SLIMseq. The shared infrastructure install requires that you separately install SLIMcore (github.com/systemsbiology/slimcore/tree/master) and RubyCAS-server (github.com/gunark/rubycas-server/tree/master). See INSTALL.rdoc for details on installing these.

The prerequisites for SLIMarray are:

• Ruby version 1.8.6 or 1.8.7

• RubyGems 1.3 or higher

• Bundler 1.0 or higher

• SLIMcore (if using the SLIMcore Authorizer plugin)

• RubyCAS-server (if using the SLIMcore Authorizer plugin)

SLIMarray is a Ruby on Rails application. Those familiar with setting up Ruby on Rails applications may find the following sufficient to get it up and running (with slimcore):

git clone git://github.com/systemsbiology/slimarray.git
cd slimarray
bundle install
bin/rake setup authorizer=slimcore
script/server

For a detailed example of how to install SLIMarray on a fresh Ubuntu 8.04 machine, see the file named INSTALL.rdoc. Installation on other operating systems should be similar.

I’ve installed it, now how do I log in?¶ ↑

With the slimsolo_authorizer, you should be able to log in as user ‘admin’ with the password ‘test’.

With the slimcore_authorizer plugin, log in in as a user that will authenticate with your RubyCAS-server install. The first user to log in will automatically be made an administrator.

How do I use the API?¶ ↑

The API documentation can be reached by adding /api to the base path to your app. So if you’re hosting SLIMarray at my-server, go to my-server/api. This describes how to use the API in general as well as documenting what calls are available and what example outputs look like.