scbi_ace is a ruby gem to read and parse ACE files containing contigs. It automatically indexes the input ace file to improve random access to contigs.

scbi_blast is a ruby gem to handle blast+ executions using pipes when possible to read data without the need of temporary files, it has been developed at [SCBI](http://www.scbi.uma.es) by Almudena Bocinos & Dario Guerrero.

scbi_cominer is a ruby gem to calculate some interesting regions and statistics from contigs

scbi_distributed_blast is a simple distribution mechanism for blast+ made on top of scbi_mapreduce. With scbi_distributed_blast you can perform distributed blasts using a cluster, a set of machines of your network or your own multi-core personal computer. It uses the same blast+ that you have already installed.

scbi_fasta is a ruby gem to read FASTA+QUAL files (DNA/RNA sequences).

scbi_headers is a gem that provides consistent text headers for command line applications.

scbi_math is a ruby gem based on narray to do some additional statistics,

scbi_plot is a simplified wrapper to create plots with gnuplot.

scbi_queue_system (SQS) handles a simple queue of jobs executions over multiple machines (clustered installation) or your own personal computer.

scbi_testcode is a ruby gem that checks if a genetic sequence is coding or not based on the testcode algorithm.

== SYNOPSIS: Allows storing scopes as names; that way you can address subsets of your model space by meaningful names. require 'scoped_proxy' # Railsers: You might want to call this in environment.rb class User < ActiveRecord::Base scoped_proxy :role do |role| { :find => { :conditions => ['role = ?', role] } } end scoped_proxy :deleted, :find => { :conditions => 'deleted_at is not null' } end admins = User.role('admin') admins.count # => 12 admins.find(:all) # => [ ... ] User.deleted.count # => a number This implementation also brings (NEW, SHINY) default proxies. That means you can have a proxy in effect when no other proxy is in effect. class User < ActiveRecord::Base default_proxy :find => { :conditions => 'deleted_at is null' } end User.find(:all) # only finds users that aren't deleted

A DataObject.rb driver for MySQL

Inline allows you to write foreign code within your ruby code. It automatically determines if the code in question has changed and builds it only when necessary. The extensions are then automatically loaded into the class/module that defines it. You can even write extra builders that will allow you to write inlined code in any language. Use Inline::C as a template and look at Module#inline for the required API.

Screwcap is a library that wraps Net::SSH and makes it easy to perform actions on remote servers.

A simple CSV(and TSV) parser to convert line into the Hash using header info.

Run RSpec with UI testing tools

Run RSpec with UI testing tools

A ruby library for accessing the SDS Rest interface

SearchableRecord is a small Ruby on Rails plugin that makes the parsing of query parameters from URLs easy for resources, allowing the requester to control the items (records) shown in the resource's representation.

Secretary is a gem who makes managing simple preference files in Ruby easier and more painless.